diff --git a/crates/uv-resolver/src/candidate_selector.rs b/crates/uv-resolver/src/candidate_selector.rs
index 7edc61545366..fdcc6c4722e8 100644
--- a/crates/uv-resolver/src/candidate_selector.rs
+++ b/crates/uv-resolver/src/candidate_selector.rs
@@ -276,7 +276,7 @@ impl CandidateSelector {
             "Selecting candidate for {package_name} with range {range} with {} remote versions",
             version_maps.iter().map(VersionMap::len).sum::<usize>(),
         );
-        let highest = self.use_highest_version(package_name);
+        let highest = self.use_highest_version(package_name, env);
 
         let allow_prerelease = match self.prerelease_strategy.allows(package_name, env) {
             AllowPrerelease::Yes => true,
@@ -359,12 +359,16 @@ impl CandidateSelector {
 
     /// By default, we select the latest version, but we also allow using the lowest version instead
     /// to check the lower bounds.
-    pub(crate) fn use_highest_version(&self, package_name: &PackageName) -> bool {
+    pub(crate) fn use_highest_version(
+        &self,
+        package_name: &PackageName,
+        env: &ResolverEnvironment,
+    ) -> bool {
         match &self.resolution_strategy {
             ResolutionStrategy::Highest => true,
             ResolutionStrategy::Lowest => false,
             ResolutionStrategy::LowestDirect(direct_dependencies) => {
-                !direct_dependencies.contains(package_name)
+                !direct_dependencies.contains(package_name, env)
             }
         }
     }
diff --git a/crates/uv-resolver/src/resolution_mode.rs b/crates/uv-resolver/src/resolution_mode.rs
index c105cfee412c..f9e12cb3fd0f 100644
--- a/crates/uv-resolver/src/resolution_mode.rs
+++ b/crates/uv-resolver/src/resolution_mode.rs
@@ -1,7 +1,4 @@
-use rustc_hash::FxHashSet;
-
-use uv_normalize::PackageName;
-
+use crate::resolver::{ForkMap, ForkSet};
 use crate::{DependencyMode, Manifest, ResolverEnvironment};
 
 #[derive(Debug, Default, Clone, Copy, PartialEq, Eq, serde::Deserialize, serde::Serialize)]
@@ -39,7 +36,7 @@ pub(crate) enum ResolutionStrategy {
     Lowest,
     /// Resolve the lowest compatible version of any direct dependencies, and the highest
     /// compatible version of any transitive dependencies.
-    LowestDirect(FxHashSet<PackageName>),
+    LowestDirect(ForkSet),
 }
 
 impl ResolutionStrategy {
@@ -52,12 +49,13 @@ impl ResolutionStrategy {
         match mode {
             ResolutionMode::Highest => Self::Highest,
             ResolutionMode::Lowest => Self::Lowest,
-            ResolutionMode::LowestDirect => Self::LowestDirect(
-                manifest
-                    .user_requirements(env, dependencies)
-                    .map(|requirement| requirement.name.clone())
-                    .collect(),
-            ),
+            ResolutionMode::LowestDirect => {
+                let mut first_party = ForkMap::default();
+                for requirement in manifest.user_requirements(env, dependencies) {
+                    first_party.add(&requirement, ());
+                }
+                Self::LowestDirect(first_party)
+            }
         }
     }
 }
diff --git a/crates/uv-resolver/src/resolver/batch_prefetch.rs b/crates/uv-resolver/src/resolver/batch_prefetch.rs
index 3acea2600588..ec2852109969 100644
--- a/crates/uv-resolver/src/resolver/batch_prefetch.rs
+++ b/crates/uv-resolver/src/resolver/batch_prefetch.rs
@@ -122,7 +122,7 @@ impl BatchPrefetcher {
                     }
                 }
                 BatchPrefetchStrategy::InOrder { previous } => {
-                    let mut range = if selector.use_highest_version(name) {
+                    let mut range = if selector.use_highest_version(name, env) {
                         Range::strictly_lower_than(previous)
                     } else {
                         Range::strictly_higher_than(previous)
diff --git a/crates/uv-resolver/src/resolver/mod.rs b/crates/uv-resolver/src/resolver/mod.rs
index 6d89cd6bd775..ba4fdafc78c1 100644
--- a/crates/uv-resolver/src/resolver/mod.rs
+++ b/crates/uv-resolver/src/resolver/mod.rs
@@ -72,7 +72,7 @@ pub use crate::resolver::provider::{
 use crate::resolver::reporter::Facade;
 pub use crate::resolver::reporter::{BuildId, Reporter};
 use crate::yanks::AllowedYanks;
-use crate::{marker, DependencyMode, Exclusions, FlatIndex, Options};
+use crate::{marker, DependencyMode, Exclusions, FlatIndex, Options, ResolutionMode};
 
 mod availability;
 mod batch_prefetch;
@@ -364,12 +364,22 @@ impl<InstalledPackages: InstalledPackagesProvider> ResolverState<InstalledPackag
                     // Walk over the selected versions, and mark them as preferences. We have to
                     // add forks back as to not override the preferences from the lockfile for
                     // the next fork
-                    for (package, version) in &resolution.nodes {
-                        preferences.insert(
-                            package.name.clone(),
-                            resolution.env.try_markers().cloned(),
-                            version.clone(),
-                        );
+                    //
+                    // If we're using a resolution mode that varies based on whether a dependency is
+                    // direct or transitive, skip preferences, as we risk adding a preference from
+                    // one fork (in which it's a transitive dependency) to another fork (in which
+                    // it's direct).
+                    if matches!(
+                        self.options.resolution_mode,
+                        ResolutionMode::Lowest | ResolutionMode::Highest
+                    ) {
+                        for (package, version) in &resolution.nodes {
+                            preferences.insert(
+                                package.name.clone(),
+                                resolution.env.try_markers().cloned(),
+                                version.clone(),
+                            );
+                        }
                     }
 
                     resolutions.push(resolution);
@@ -1832,6 +1842,10 @@ impl<InstalledPackages: InstalledPackagesProvider> ResolverState<InstalledPackag
                     }
                 };
 
+                // We don't have access to the fork state when prefetching, so assume that
+                // pre-release versions are allowed.
+                let env = ResolverEnvironment::universal(vec![]);
+
                 // Try to find a compatible version. If there aren't any compatible versions,
                 // short-circuit.
                 let Some(candidate) = self.selector.select(
@@ -1841,9 +1855,7 @@ impl<InstalledPackages: InstalledPackagesProvider> ResolverState<InstalledPackag
                     &self.preferences,
                     &self.installed_packages,
                     &self.exclusions,
-                    // We don't have access to the fork state when prefetching, so assume that
-                    // pre-release versions are allowed.
-                    &ResolverEnvironment::universal(vec![]),
+                    &env,
                 ) else {
                     return Ok(None);
                 };
@@ -1857,7 +1869,7 @@ impl<InstalledPackages: InstalledPackagesProvider> ResolverState<InstalledPackag
                 // often leads to failed attempts to build legacy versions of packages that are
                 // incompatible with modern build tools.
                 if dist.wheel().is_none() {
-                    if !self.selector.use_highest_version(&package_name) {
+                    if !self.selector.use_highest_version(&package_name, &env) {
                         if let Some((lower, _)) = range.iter().next() {
                             if lower == &Bound::Unbounded {
                                 debug!("Skipping prefetch for unbounded minimum-version range: {package_name} ({range})");
diff --git a/crates/uv/tests/it/pip_compile.rs b/crates/uv/tests/it/pip_compile.rs
index 0cfcc8194a99..9352bacf4663 100644
--- a/crates/uv/tests/it/pip_compile.rs
+++ b/crates/uv/tests/it/pip_compile.rs
@@ -12686,3 +12686,82 @@ fn unsupported_requires_python_dynamic_metadata() -> Result<()> {
 
     Ok(())
 }
+
+/// Perform a universal resolution with a constraint, where the constraint itself has a marker.
+#[test]
+fn lowest_direct_fork() -> Result<()> {
+    let context = TestContext::new("3.10");
+    let requirements_in = context.temp_dir.child("requirements.in");
+    requirements_in.write_str(indoc::indoc! {r"
+        pycountry >= 22.1.10
+        setuptools >= 50.0.0 ; python_version >= '3.12'
+    "})?;
+
+    uv_snapshot!(context.filters(), windows_filters=false, context.pip_compile()
+            .arg("requirements.in")
+            .arg("--universal")
+            .arg("--resolution")
+            .arg("lowest-direct"), @r###"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+    # This file was autogenerated by uv via the following command:
+    #    uv pip compile --cache-dir [CACHE_DIR] requirements.in --universal --resolution lowest-direct
+    pycountry==22.1.10
+        # via -r requirements.in
+    setuptools==50.0.0 ; python_full_version >= '3.12'
+        # via
+        #   -r requirements.in
+        #   pycountry
+    setuptools==69.2.0 ; python_full_version < '3.12'
+        # via
+        #   -r requirements.in
+        #   pycountry
+
+    ----- stderr -----
+    Resolved 3 packages in [TIME]
+    "###
+    );
+
+    Ok(())
+}
+
+/// Perform a universal resolution with a constraint, where the constraint itself has a marker.
+#[test]
+fn lowest_fork() -> Result<()> {
+    let context = TestContext::new("3.10");
+    let requirements_in = context.temp_dir.child("requirements.in");
+    requirements_in.write_str(indoc::indoc! {r"
+        pycountry >= 22.1.10
+        setuptools >= 50.0.0 ; python_version >= '3.12'
+    "})?;
+
+    uv_snapshot!(context.filters(), windows_filters=false, context.pip_compile()
+            .arg("requirements.in")
+            .arg("--universal")
+            .arg("--resolution")
+            .arg("lowest"), @r###"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+    # This file was autogenerated by uv via the following command:
+    #    uv pip compile --cache-dir [CACHE_DIR] requirements.in --universal --resolution lowest
+    pycountry==22.1.10
+        # via -r requirements.in
+    setuptools==0.7.2 ; python_full_version < '3.12'
+        # via
+        #   -r requirements.in
+        #   pycountry
+    setuptools==50.0.0 ; python_full_version >= '3.12'
+        # via
+        #   -r requirements.in
+        #   pycountry
+
+    ----- stderr -----
+    Resolved 3 packages in [TIME]
+    warning: The transitive dependency `setuptools` is unpinned. Consider setting a lower bound with a constraint when using `--resolution-strategy lowest` to avoid using outdated versions.
+    "###
+    );
+
+    Ok(())
+}