diff --git a/light9/rdfdb/graphfile.py b/light9/rdfdb/graphfile.py
--- a/light9/rdfdb/graphfile.py
+++ b/light9/rdfdb/graphfile.py
@@ -26,6 +26,8 @@ class GraphFile(object):
 
         self.lastWriteTimestamp = 0 # mtime from the last time _we_ wrote
 
+        self.namespaces = {}
+        
         if not os.path.exists(path):
             # can't start notify until file exists
             try:
@@ -126,6 +128,7 @@ class GraphFile(object):
                 return
 
             new.parse(location=self.path, format='n3')
+            self.namespaces.update(dict(new.namespaces()))
         except SyntaxError as e:
             print e
             traceback.print_exc()
@@ -177,6 +180,8 @@ class GraphFile(object):
         tmpOut = self.path + ".rdfdb-temp"
         f = open(tmpOut, 'w')
         t1 = time.time()
+        for p, n in self.namespaces.items():
+            self.graphToWrite.bind(p, n)
         self.graphToWrite.serialize(destination=f, format='n3')
         serializeTime = time.time() - t1
         f.close()
diff --git a/light9/rdfdb/graphfile_test.py b/light9/rdfdb/graphfile_test.py
new file mode 100644
--- /dev/null
+++ b/light9/rdfdb/graphfile_test.py
@@ -0,0 +1,39 @@
+import unittest
+import mock
+import tempfile
+from rdflib import URIRef, Graph
+from light9.rdfdb.graphfile import GraphFile
+
+class TestGraphFileOutput(unittest.TestCase):
+    def testMaintainsN3PrefixesFromInput(self):
+        tf = tempfile.NamedTemporaryFile(suffix='_test.n3')
+        tf.write('''
+        @prefix : <http://example.com/> .
+        @prefix n: <http://example.com/n/> .
+        :foo n:bar :baz .
+        ''')
+        tf.flush()
+
+        def getSubgraph(uri):
+            return Graph()
+        gf = GraphFile(mock.Mock(), tf.name, URIRef('uri'), mock.Mock(), getSubgraph)
+        gf.reread()
+        
+        newGraph = Graph()
+        newGraph.add((URIRef('http://example.com/boo'),
+                      URIRef('http://example.com/n/two'),
+                      URIRef('http://example.com/other/ns')))
+        gf.dirty(newGraph)
+        gf.flush()
+        wroteContent = open(tf.name).read()
+        self.assertEqual('''@prefix : <http://example.com/> .
+@prefix n: <http://example.com/n/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+:boo n:two <http://example.com/other/ns> .
+
+''', wroteContent)
+
diff --git a/makefile b/makefile
--- a/makefile
+++ b/makefile
@@ -1,4 +1,4 @@
-NOSEARGS="--no-path-adjustment light9.rdfdb.rdflibpatch light9.rdfdb.patch light9.effecteval.test_effect light9.collector"
+NOSEARGS="--no-path-adjustment light9.rdfdb.rdflibpatch light9.rdfdb.patch light9.effecteval.test_effect light9.collector light9.rdfdb.graphfile_test"
 
 tests:
 	eval env/bin/nosetests -x $(NOSEARGS)