diff --git a/pyfaidx/__init__.py b/pyfaidx/__init__.py
index 6fa3dea..8c3de92 100644
--- a/pyfaidx/__init__.py
+++ b/pyfaidx/__init__.py
@@ -21,7 +21,7 @@
 
 dna_bases = re.compile(r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)')
 
-__version__ = '0.3.9'
+__version__ = '0.3.9.1'
 
 
 class FastaIndexingError(Exception):
@@ -205,7 +205,7 @@ def __init__(self, filename, default_seq=None, key_function=None,
 
         self.mutable = mutable
 
-        if os.path.exists(self.indexname) and getmtime(self.indexname) > getmtime(self.filename):
+        if os.path.exists(self.indexname) and getmtime(self.indexname) >= getmtime(self.filename):
             self.read_fai(split_char)
         else:
             try: