diff --git a/modules/EnsEMBL/Draw/GlyphSet/Vsynteny.pm b/modules/EnsEMBL/Draw/GlyphSet/Vsynteny.pm
index 1325f8383a..32ba86487f 100644
--- a/modules/EnsEMBL/Draw/GlyphSet/Vsynteny.pm
+++ b/modules/EnsEMBL/Draw/GlyphSet/Vsynteny.pm
@@ -101,19 +101,55 @@ sub _init {
   my $highlights_main = { $chr => [] };
   my $CANSEE_OTHER = $config->{'other_species_installed'};
 
+  # When working with a synteny dataset such as the Hsap synteny, we need to be able to distinguish
+  # between the main and other synteny regions, even if both are from the same genome. Moreover, we
+  # may encounter synteny pairs between two regions on the same chromosome in the same genome. In
+  # such cases, the Compara API may return the same synteny pair twice, without distinction between
+  # the two syntenic regions. To help make sense of all this, we generate a synteny region key for
+  # each region of the main chromosome that is in a synteny pair, so that we can then sort the
+  # synteny regions in order to 'thread' them along the main chromosome.
+  my %syntenies_by_main_region;
   foreach my $synteny_region (@$synteny_data) {
-    my ($main_dfr, $other_dfr);
+    my ($dfr1, $dfr2) = @{$synteny_region->get_all_DnaFragRegions};
 
-    foreach my $dfr (@{$synteny_region->get_all_DnaFragRegions}) {
-      if (lc($self_production_name) eq lc($dfr->dnafrag->genome_db->name) and $dfr->dnafrag->genome_db->name eq $other_production_name) {
-        $main_dfr = $dfr;
-        $other_dfr = $dfr;
-      } elsif ($dfr->dnafrag->genome_db->name eq $other_production_name) {
-        $other_dfr = $dfr;
-      } else {
-        $main_dfr = $dfr;
-      }
+    if (lc($dfr1->dnafrag->genome_db->name) eq lc($self_production_name) && $dfr1->dnafrag->name eq $chr) {
+
+      my $dfr1_synteny_region_key = join(
+        ':',
+        $synteny_region->dbID,
+        $dfr1->dnafrag->dbID,
+        $dfr1->dnafrag_start,
+        $dfr1->dnafrag_end,
+        $dfr1->dnafrag_strand,
+      );
+
+      $syntenies_by_main_region{$dfr1_synteny_region_key} = [$dfr1_synteny_region_key, $dfr1, $dfr2];
     }
+
+    if (lc($dfr2->dnafrag->genome_db->name) eq lc($self_production_name) && $dfr2->dnafrag->name eq $chr) {
+
+      my $dfr2_synteny_region_key = join(
+        ':',
+        $synteny_region->dbID,
+        $dfr2->dnafrag->dbID,
+        $dfr2->dnafrag_start,
+        $dfr2->dnafrag_end,
+        $dfr2->dnafrag_strand,
+      );
+
+      $syntenies_by_main_region{$dfr2_synteny_region_key} = [$dfr2_synteny_region_key, $dfr2, $dfr1];
+    }
+  }
+
+  my @synteny_regions = sort {
+    $a->[1]->dnafrag_start <=> $b->[1]->dnafrag_start
+    || $b->[1]->dnafrag_end <=> $a->[1]->dnafrag_end
+    || $b->[1]->dnafrag_strand <=> $a->[1]->dnafrag_strand
+    || $a->[0] cmp $b->[0]
+  } values %syntenies_by_main_region;
+
+  foreach my $synteny_region (@synteny_regions) {
+    my ($synteny_region_key, $main_dfr, $other_dfr) = @$synteny_region;
     
     my $other_chr = $other_dfr->dnafrag->name;
     
@@ -148,7 +184,7 @@ sub _init {
     });
     
     push @{$highlights_main->{$chr}}, {
-      'id'     => $synteny_region->dbID,
+      'id'     => $synteny_region_key,
       'start'  => $main_dfr->dnafrag_start,
       'end'    => $main_dfr->dnafrag_end,
       'col'    => $COL,
@@ -173,7 +209,7 @@ sub _init {
       
       push @{$highlights_secondary->{$other_chr}}, {
         'rel_ori' => $main_dfr->dnafrag_strand * $other_dfr->dnafrag_strand,
-        'id'      => $synteny_region->dbID,
+        'id'      => $synteny_region_key,
         'start'   => $other_dfr->dnafrag_start,
         'end'     => $other_dfr->dnafrag_end,
         'col'     => $COL,
diff --git a/modules/EnsEMBL/Web/Component/Location/SyntenyImage.pm b/modules/EnsEMBL/Web/Component/Location/SyntenyImage.pm
index 2a56013916..6f5d2c579c 100644
--- a/modules/EnsEMBL/Web/Component/Location/SyntenyImage.pm
+++ b/modules/EnsEMBL/Web/Component/Location/SyntenyImage.pm
@@ -37,6 +37,7 @@ sub content {
   my $hub     = $self->hub;
   my $object  = $self->object || $self->hub->core_object('location');
   my $species = $hub->species;
+  my $this_prodname = $hub->species_defs->get_config($species, 'SPECIES_PRODUCTION_NAME');
   my %synteny = $hub->species_defs->multi('DATABASE_COMPARA', 'SYNTENY');
   my $other   = $self->hub->otherspecies; 
   my $other_prodname = $hub->species_defs->get_config($other, 'SPECIES_PRODUCTION_NAME');
@@ -44,7 +45,7 @@ sub content {
   my %chr_1   = map { $_, 1 } @{$hub->species_defs->ENSEMBL_CHROMOSOMES || []};
   my %chr_2   = map { $_, 1 } @{$hub->species_defs->get_config($other, 'ENSEMBL_CHROMOSOMES') || []};
   
-  unless ($synteny{$other_prodname}) {
+  unless ($synteny{$this_prodname}{$other_prodname}) {
     $hub->problem('fatal', "Can't display synteny",  "There is no synteny data for these two species ($species and $other)");
     return undef;
   }
@@ -52,23 +53,19 @@ sub content {
   my $ka         = $hub->get_adaptor('get_KaryotypeBandAdaptor', 'core', $species);
   my $ka2        = $hub->get_adaptor('get_KaryotypeBandAdaptor', 'core', $other);
   my $compara_db = $hub->database('compara');
-  my $raw_data   = $object->chromosome->get_all_compara_Syntenies($other, undef, $compara_db);   
   my $chr_length = $object->chromosome->length;
-  my $other_chr;
-
-  OUTER:
-  foreach my $synteny_region (@$raw_data) {
-    foreach my $dfr (@{$synteny_region->get_all_DnaFragRegions}) {
-      # Check if any of the synteny regions map to a chromosome in the other species
-      if ($dfr->dnafrag->genome_db->name eq $other_prodname && $chr_2{$dfr->dnafrag->name}) {
-        $other_chr = 1;
-        last OUTER;
-      }
-    }
+
+  my $genome_dba = $compara_db->get_GenomeDBAdaptor();
+  my @synteny_gdbs = ($genome_dba->fetch_by_name_assembly($this_prodname));
+  if ($other_prodname ne $this_prodname) {
+    push(@synteny_gdbs, $genome_dba->fetch_by_name_assembly($other_prodname));
   }
 
+  my $mlss = $compara_db->get_MethodLinkSpeciesSetAdaptor->fetch_by_method_link_type_GenomeDBs('SYNTENY', \@synteny_gdbs);
+  my $raw_data = $compara_db->get_SyntenyRegionAdaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss, $object->chromosome);
+
   my $image_html;
-  if ($chr_1{$chr} && $other_chr) {
+  if (scalar(@$raw_data) > 0) {
 
     my ($localgenes, $offset) = $object->get_synteny_local_genes;
     my $loc = (@$localgenes ? $localgenes->[0]->start + $object->seq_region_start : 1); # Jump loc to the location of the genes
@@ -102,7 +99,7 @@ sub content {
     $image_html = $image->render;
   }
   else {
-    $image_html = $self->info_panel("Unassembled chromosomes", "<p>No image can be drawn, because the syntenous species has no assembled chromosomes.</p>");
+    $image_html = $self->info_panel("Unavailable synteny regions", "<p>No image can be drawn, because this chromosome lacks synteny regions with the selected species.</p>");
   }
   my $chr_form = $self->chromosome_form('Vsynteny');