diff --git a/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/OntologyManager.java b/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/OntologyManager.java
index 6b14b5af..c78f27aa 100644
--- a/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/OntologyManager.java
+++ b/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/OntologyManager.java
@@ -21,6 +21,7 @@ public class OntologyManager {
   private Map<String, IRI> locationToIriMapping = new HashMap<>();
   private Set<OWLOntology> ontologies;
   private Set<MissingImport> missingImports;
+  private Map<String, String> sourceNamespacesMap = new HashMap<>();
 
   public OWLOntology getOntology() {
     return ontology;
@@ -63,4 +64,12 @@ public Set<MissingImport> getMissingImports() {
   public void setMissingImports(Set<MissingImport> missingImports) {
     this.missingImports = missingImports;
   }
+
+  public Map<String, String> getSourceNamespacesMap() {
+    return sourceNamespacesMap;
+  }
+
+  public void setSourceNamespacesMap(Map<String, String> sourceNamespacesMap) {
+    this.sourceNamespacesMap = sourceNamespacesMap;
+  }
 }
\ No newline at end of file
diff --git a/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/loader/CommandLineOntologyLoader.java b/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/loader/CommandLineOntologyLoader.java
index 265daedb..b4e4f9e0 100644
--- a/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/loader/CommandLineOntologyLoader.java
+++ b/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/loader/CommandLineOntologyLoader.java
@@ -16,9 +16,11 @@
 import org.edmcouncil.spec.ontoviewer.core.ontology.loader.listener.MissingImportListenerImpl;
 import org.edmcouncil.spec.ontoviewer.core.ontology.loader.zip.ViewerZipFilesOperations;
 import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.formats.PrefixDocumentFormat;
 import org.semanticweb.owlapi.model.AddImport;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.MissingImportHandlingStrategy;
+import org.semanticweb.owlapi.model.OWLDocumentFormat;
 import org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyDocumentAlreadyExistsException;
@@ -120,12 +122,18 @@ private LoadedOntologyData loadOntologiesFromIris(OWLOntologyManager ontologyMan
     ontologyManager.addMissingImportListener(missingImportListenerImpl);
 
     var umbrellaOntology = ontologyManager.createOntology();
+    Map<String, String> sourceNamespacesMap = new HashMap<>();
 
     for (OntologySource ontologySource : ontologySources) {
       LOGGER.debug("Loading ontology from IRI '{}'...", ontologySource);
 
       try {
         var currentOntology = ontologyManager.loadOntology(ontologySource.getAsIri());
+        OWLDocumentFormat ontologyFormat = ontologyManager.getOntologyFormat(currentOntology);
+        if (ontologyFormat != null) {
+          sourceNamespacesMap.putAll(ontologyFormat.asPrefixOWLDocumentFormat().getPrefixName2PrefixMap());
+        }
+
         var ontologyIri = currentOntology.getOntologyID().getOntologyIRI().orElse(ontologySource.getAsIri());
         ontologyIrisToPaths.put(ontologyIri, ontologySource.getAsIri());
         ontologyPathsToIris.put(ontologySource.getOriginalLocation(), ontologyIri);
@@ -145,6 +153,6 @@ private LoadedOntologyData loadOntologiesFromIris(OWLOntologyManager ontologyMan
       }
     }
 
-    return new LoadedOntologyData(umbrellaOntology, ontologyIrisToPaths, ontologyPathsToIris);
+    return new LoadedOntologyData(umbrellaOntology, ontologyIrisToPaths, ontologyPathsToIris, sourceNamespacesMap);
   }
-}
+}
\ No newline at end of file
diff --git a/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/loader/LoadedOntologyData.java b/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/loader/LoadedOntologyData.java
index cd0dd7c3..f590bf82 100644
--- a/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/loader/LoadedOntologyData.java
+++ b/onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/loader/LoadedOntologyData.java
@@ -14,20 +14,23 @@ public class LoadedOntologyData {
   private final Map<IRI, IRI> irisToPathsMapping;
   private final Map<String, IRI> pathsToIrisMapping;
   private final LoadingDetails loadingDetails;
+  private final Map<String, String> sourceNamespacesMap;
 
   public LoadedOntologyData(OWLOntology ontology, Map<IRI, IRI> irisToPathsMapping) {
     this.ontology = ontology;
     this.irisToPathsMapping = irisToPathsMapping;
     this.pathsToIrisMapping = new HashMap<>();
     this.loadingDetails = new LoadingDetails(Collections.emptyList());
+    this.sourceNamespacesMap = new HashMap<>();
   }
 
   public LoadedOntologyData(OWLOntology ontology, Map<IRI, IRI> irisToPathsMapping,
-      Map<String, IRI> pathsToIrisMapping) {
+      Map<String, IRI> pathsToIrisMapping, Map<String, String> sourceNamespacesMap) {
     this.ontology = ontology;
     this.irisToPathsMapping = irisToPathsMapping;
     this.pathsToIrisMapping = pathsToIrisMapping;
     this.loadingDetails = new LoadingDetails(Collections.emptyList());
+    this.sourceNamespacesMap = sourceNamespacesMap;
   }
 
   public LoadedOntologyData(LoadedOntologyData loadedOntologyData, LoadingDetails loadingDetails) {
@@ -35,6 +38,7 @@ public LoadedOntologyData(LoadedOntologyData loadedOntologyData, LoadingDetails
     this.irisToPathsMapping = loadedOntologyData.getIrisToPathsMapping();
     this.pathsToIrisMapping = loadedOntologyData.getPathsToIrisMapping();
     this.loadingDetails = loadingDetails;
+    this.sourceNamespacesMap = loadedOntologyData.getSourceNamespacesMap();
   }
 
   public OWLOntology getOntology() {
@@ -53,6 +57,10 @@ public LoadingDetails getLoadingDetails() {
     return loadingDetails;
   }
 
+  public Map<String, String> getSourceNamespacesMap() {
+    return sourceNamespacesMap;
+  }
+
   public static class LoadingDetails {
 
     private final List<MissingImport> missingImports;
@@ -65,4 +73,4 @@ public List<MissingImport> getMissingImports() {
       return missingImports;
     }
   }
-}
+}
\ No newline at end of file
diff --git a/onto-viewer-toolkit/src/main/java/org/edmcouncil/spec/ontoviewer/toolkit/OntoViewerToolkitCommandLine.java b/onto-viewer-toolkit/src/main/java/org/edmcouncil/spec/ontoviewer/toolkit/OntoViewerToolkitCommandLine.java
index b6aae370..aefc22a0 100644
--- a/onto-viewer-toolkit/src/main/java/org/edmcouncil/spec/ontoviewer/toolkit/OntoViewerToolkitCommandLine.java
+++ b/onto-viewer-toolkit/src/main/java/org/edmcouncil/spec/ontoviewer/toolkit/OntoViewerToolkitCommandLine.java
@@ -190,9 +190,12 @@ public void run(String... args) throws Exception {
         if (outputOption.isPresent()) {
           var output = outputOption.get();
           LOGGER.info("Saving merged ontology to '{}'...", output);
+          RDFXMLDocumentFormat outputDocumentFormat = new RDFXMLDocumentFormat();
+          ontologyManager.getSourceNamespacesMap().forEach(outputDocumentFormat::setPrefix);
+
           owlOntologyManager.saveOntology(
               mergedOntology,
-              new RDFXMLDocumentFormat(),
+              outputDocumentFormat,
               IRI.create(new File(output)));
         } else {
           throw new OntoViewerToolkitRuntimeException("Error: 'output' argument is not present.");
@@ -330,6 +333,7 @@ private LoadedOntologyData loadOntology(Goal goal) throws OntoViewerToolkitExcep
 
       ontologyManager.updateOntology(loadedOntology);
       ontologyManager.setLocationToIriMapping(loadedOntologyData.getPathsToIrisMapping());
+      ontologyManager.setSourceNamespacesMap(loadedOntologyData.getSourceNamespacesMap());
       if (shouldPopulateOntologyResources(goal)) {
         resourcesPopulate.populateOntologyResources();
       }