diff --git a/Lib/fontTools/subset.py b/Lib/fontTools/subset.py
index 44bc06948..17f0e307f 100644
--- a/Lib/fontTools/subset.py
+++ b/Lib/fontTools/subset.py
@@ -643,7 +643,8 @@ def subset_glyphs(self, s):
   if self.Format == 1:
     indices = self.Coverage.subset(s.glyphs)
     rss = getattr(self, c.RuleSet)
-    rss = [rss[i] for i in indices]
+    rssCount = getattr(self, c.RuleSetCount)
+    rss = [rss[i] for i in indices if i < rssCount]
     for rs in rss:
       if not rs: continue
       ss = getattr(rs, c.Rule)
@@ -652,8 +653,10 @@ def subset_glyphs(self, s):
               for glist in c.RuleData(r))]
       setattr(rs, c.Rule, ss)
       setattr(rs, c.RuleCount, len(ss))
-    # Prune empty subrulesets
-    rss = [rs for rs in rss if rs and getattr(rs, c.Rule)]
+    # Prune empty rulesets
+    indices = [i for i,rs in enumerate(rss) if rs and getattr(rs, c.Rule)]
+    self.Coverage.remap(indices)
+    rss = [rss[i] for i in indices]
     setattr(self, c.RuleSet, rss)
     setattr(self, c.RuleSetCount, len(rss))
     return bool(rss)
@@ -687,7 +690,7 @@ def subset_glyphs(self, s):
         c.SetRuleData(r, [[klass_map.index(k) for k in klist]
                for klass_map,klist in zip(klass_maps, c.RuleData(r))])
 
-    # Prune empty subrulesets
+    # Prune empty rulesets
     rss = [rs if rs and getattr(rs, c.Rule) else None for rs in rss]
     while rss and rss[-1] is None:
       del rss[-1]