diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index bc03274c4..aa8e33e6e 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -215,6 +215,10 @@ impl Collection {
         assert_eq!(sig.signatures.len(), 1);
         Ok(sig)
     }
+
+    pub fn intersect_manifest(&mut self, mf: &Manifest) {
+        self.manifest = self.manifest.intersect_manifest(mf);
+    }
 }
 
 impl Select for Collection {
@@ -233,6 +237,7 @@ mod test {
     use super::Collection;
 
     use crate::encodings::HashFunctions;
+    use crate::manifest::Manifest;
     use crate::prelude::Select;
     use crate::selection::Selection;
     use crate::signature::Signature;
@@ -358,6 +363,32 @@ mod test {
         assert_eq!(cl.len(), 0);
     }
 
+    #[test]
+    fn collection_intersect_manifest() {
+        // load test sigs
+        let mut filename = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
+        // four num=500 sigs
+        filename.push("../../tests/test-data/genome-s11.fa.gz.sig");
+        let file = File::open(filename).unwrap();
+        let reader = BufReader::new(file);
+        let sigs: Vec<Signature> = serde_json::from_reader(reader).expect("Loading error");
+        assert_eq!(sigs.len(), 4);
+        // load sigs into collection + select compatible signatures
+        let mut cl = Collection::from_sigs(sigs).unwrap();
+        // all sigs should remain
+        assert_eq!(cl.len(), 4);
+
+        // grab first record
+        let manifest = cl.manifest();
+        let record = manifest.iter().next().unwrap().clone();
+        let vr = vec![record];
+
+        // now intersect:
+        let manifest2 = Manifest::from(vr);
+        cl.intersect_manifest(&manifest2);
+        assert_eq!(cl.len(), 1);
+    }
+
     #[test]
     fn sigstore_sig_from_record() {
         // load test sigs
diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 0a84a3e49..2f1eca7e0 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -1,4 +1,6 @@
+use std::collections::HashSet;
 use std::fs::File;
+use std::hash::{Hash, Hasher};
 use std::io::{BufRead, BufReader, Read, Write};
 use std::ops::Deref;
 
@@ -17,7 +19,7 @@ use crate::Result;
 
 /// Individual manifest record, containing information about sketches.
 
-#[derive(Debug, Serialize, Deserialize, Clone, CopyGetters, Getters, Setters, PartialEq, Eq)]
+#[derive(Debug, Serialize, Deserialize, Clone, CopyGetters, Getters, Setters)]
 pub struct Record {
     #[getset(get = "pub", set = "pub")]
     internal_location: PathBuf,
@@ -176,6 +178,37 @@ impl Record {
     }
 }
 
+impl PartialEq for Record {
+    // match everything but internal_location
+    fn eq(&self, other: &Self) -> bool {
+        self.md5 == other.md5
+            && self.ksize == other.ksize
+            && self.moltype == other.moltype
+            && self.scaled == other.scaled
+            && self.num == other.num
+            && self.n_hashes == other.n_hashes
+            && self.with_abundance == other.with_abundance
+            && self.name == other.name
+            && self.filename == other.filename
+    }
+}
+
+impl Eq for Record {}
+
+impl Hash for Record {
+    fn hash<H: Hasher>(&self, state: &mut H) {
+        self.md5.hash(state);
+        self.ksize.hash(state);
+        self.moltype.hash(state);
+        self.scaled.hash(state);
+        self.num.hash(state);
+        self.n_hashes.hash(state);
+        self.with_abundance.hash(state);
+        self.name.hash(state);
+        self.filename.hash(state);
+    }
+}
+
 impl Manifest {
     pub fn from_reader<R: Read>(rdr: R) -> Result<Self> {
         let mut records = vec![];
@@ -209,6 +242,20 @@ impl Manifest {
     pub fn iter(&self) -> impl Iterator<Item = &Record> {
         self.records.iter()
     }
+
+    pub fn intersect_manifest(&self, other: &Manifest) -> Self {
+        // extract tuples from other mf:
+        let pairs: HashSet<_> = other.iter().collect();
+
+        let records = self
+            .records
+            .iter()
+            .filter(|row| pairs.contains(row))
+            .cloned()
+            .collect();
+
+        Self { records }
+    }
 }
 
 impl Select for Manifest {
@@ -521,4 +568,60 @@ mod test {
         let scaled100 = manifest.select(&selection).unwrap();
         assert_eq!(scaled100.len(), 6);
     }
+
+    #[test]
+    fn manifest_intersect() {
+        let temp_dir = TempDir::new().unwrap();
+        let utf8_output = PathBuf::from_path_buf(temp_dir.path().to_path_buf())
+            .expect("Path should be valid UTF-8");
+        let filename = utf8_output.join("sig-pathlist.txt");
+        // build sig filenames
+        let base_path = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
+        let test_sigs = vec![
+            "../../tests/test-data/47.fa.sig",
+            "../../tests/test-data/63.fa.sig",
+        ];
+
+        let full_paths: Vec<_> = test_sigs
+            .into_iter()
+            .map(|sig| base_path.join(sig))
+            .collect();
+
+        // write a file in test directory with a filename on each line
+        let mut pathfile = File::create(&filename).unwrap();
+        for sigfile in &full_paths {
+            writeln!(pathfile, "{}", sigfile).unwrap();
+        }
+
+        // load into manifest
+        let manifest = Manifest::from(&filename);
+        assert_eq!(manifest.len(), 2);
+
+        // now do just one sketch -
+        let test_sigs2 = vec!["../../tests/test-data/63.fa.sig"];
+
+        let filename2 = utf8_output.join("sig-pathlist-single.txt");
+
+        let full_paths: Vec<_> = test_sigs2
+            .into_iter()
+            .map(|sig| base_path.join(sig))
+            .collect();
+
+        let mut pathfile2 = File::create(&filename2).unwrap();
+        for sigfile in &full_paths {
+            writeln!(pathfile2, "{}", sigfile).unwrap();
+        }
+
+        // load into another manifest
+        let manifest2 = Manifest::from(&filename2);
+        assert_eq!(manifest2.len(), 1);
+
+        // intersect with itself => same.
+        let new_mf = manifest2.intersect_manifest(&manifest);
+        assert_eq!(new_mf.len(), 1);
+
+        // intersect with other => single.
+        let new_mf = manifest.intersect_manifest(&manifest2);
+        assert_eq!(new_mf.len(), 1);
+    }
 }