diff --git a/src/main/java/org/opentripplanner/graph_builder/module/GtfsFeedId.java b/src/main/java/org/opentripplanner/graph_builder/module/GtfsFeedId.java
index dd930d7190c..a9522892e43 100644
--- a/src/main/java/org/opentripplanner/graph_builder/module/GtfsFeedId.java
+++ b/src/main/java/org/opentripplanner/graph_builder/module/GtfsFeedId.java
@@ -19,7 +19,7 @@ public class GtfsFeedId {
     private static int FEED_ID_COUNTER = 1;
 
     /**
-     * A Map that keeps track of which feed ids were generated in the {@link Builder#build()} method to make sure there
+     * A Set that keeps track of which feed ids were generated in the {@link Builder#build()} method to make sure there
      * are no duplicates.
      */
     private static final Set<String> seenIds = new HashSet<>();
@@ -118,11 +118,14 @@ protected String cleanId(String id) {
         public GtfsFeedId build() {
             boolean autoGenerated = false;
             id = cleanId(id);
+            // auto-generate a new ID if it is null or a zero-length string
             if (id == null || id.trim().length() == 0) {
                 id = String.valueOf(FEED_ID_COUNTER);
                 autoGenerated = true;
             }
-            if (seenIds.contains(id)) {
+            // add the feed ID to the set of IDs seen so far. If the set already contained the ID, throw an error in
+            // order to avoid using duplicate feed IDs.
+            if (!seenIds.add(id)) {
                 throw new RuntimeException(
                     String.format(
                         "A duplicate Feed ID of `%s` was encountered when loading GTFS data!",
@@ -130,7 +133,6 @@ public GtfsFeedId build() {
                     )
                 );
             }
-            seenIds.add(id);
             FEED_ID_COUNTER++;
             return new GtfsFeedId(id, autoGenerated);
         }
diff --git a/src/main/java/org/opentripplanner/graph_builder/module/GtfsModule.java b/src/main/java/org/opentripplanner/graph_builder/module/GtfsModule.java
index 0e91494232b..86fe4862763 100644
--- a/src/main/java/org/opentripplanner/graph_builder/module/GtfsModule.java
+++ b/src/main/java/org/opentripplanner/graph_builder/module/GtfsModule.java
@@ -233,7 +233,7 @@ private GtfsMutableRelationalDao loadBundle(GtfsBundle gtfsBundle)
         if (bundleFilenamesWithAutoGeneratedFeedId.contains(bundleFilename)) {
             throw new RuntimeException(
                 String.format(
-                    "There are at least 2 bundles with the name `%s` that lack a feed_id value in a record in the feed_info.txt table. This will result in non-deterministic Feed ID generation!",
+                    "There are at least 2 GTFS bundles with the name `%s` that lack a feed_id value in a record in the feed_info.txt table. This will result in non-deterministic Feed ID generation!",
                     bundleFilename
                 )
             );
@@ -244,7 +244,8 @@ private GtfsMutableRelationalDao loadBundle(GtfsBundle gtfsBundle)
         }
 
         // Read the agency table to determine if there is a single agency entry without an agency ID. This is used later
-        // to determine whether an agency ID was auto-generated. According to the GTFS spec, if there are multiple
+        // to determine whether an agency ID was auto-generated (it will be auto-generated to the bundle's feed ID if
+        // the agency ID is missing in a single-agency feed). According to the GTFS spec, if there are multiple
         // agencies, then they must have an agency ID. Therefore, it is only necessary to read the first record.
         boolean agencyFileContainedOneAgencyWithoutId = false;
         InputStream agencyInputStream = gtfsBundle.getCsvInputSource().getResource("agency.txt");
@@ -264,6 +265,7 @@ private GtfsMutableRelationalDao loadBundle(GtfsBundle gtfsBundle)
         reader.setInputSource(gtfsBundle.getCsvInputSource());
         reader.setEntityStore(store);
         reader.setInternStrings(true);
+        // Set the default Agency ID to be the Feed ID of this bundle.
         reader.setDefaultAgencyId(gtfsFeedId.getId());
 
         if (LOG.isDebugEnabled())
diff --git a/src/test/java/org/opentripplanner/graph_builder/module/GtfsFeedIdTest.java b/src/test/java/org/opentripplanner/graph_builder/module/GtfsFeedIdTest.java
new file mode 100644
index 00000000000..26d98bb306b
--- /dev/null
+++ b/src/test/java/org/opentripplanner/graph_builder/module/GtfsFeedIdTest.java
@@ -0,0 +1,21 @@
+package org.opentripplanner.graph_builder.module;
+
+import org.junit.Test;
+
+public class GtfsFeedIdTest {
+    @Test
+    public void shouldUseProvidedFeedId() {
+        assert(new GtfsFeedId.Builder().id("abcd").build().getId().equals("abcd"));
+    }
+
+    @Test
+    public void canAutoGenerateFeedId() {
+        assert(Integer.valueOf(new GtfsFeedId.Builder().id("").build().getId()) > 0);
+    }
+
+    @Test(expected = RuntimeException.class)
+    public void throwsErrorOnDuplicateFeedId() {
+        new GtfsFeedId.Builder().id("abc123").build();
+        new GtfsFeedId.Builder().id("abc123").build();
+    }
+}
\ No newline at end of file