The cave should already been in use as a Church since the 16th century. Records of the period, namely the cronicle in verse of Marino Tzanes Bounialis, on the Cretan wars of 1669, mention it . The chapel was dedicated a Saint that has been the patron of builders as well of sailors and also of the poor.
The Saint has also been a protector against plague. A disease that had tarnished, several times over, the city of Rethymnon. He has also protected the inhabitants more recently when the cave proved to be a refuge during the brutal bombardments of the WWII.
Sadly the original paintings that were decorating the Cave Chapel of St Spyridon have been distroyed and replaced by more recent but still the chapel is defently worth visiting as part of an excursion Rethymnon and a short climb up to the to the beautiful Fortezza Castle (that deserves its own, separate blog post)
The little chapel is opened daily.
You may approach the chapel from the road on the west side of the fortress. The feast of the saint is commenorated on December 12th
You may also watch this very informative video with the chapel (published by Orthodoxy Ancienty Nature History in youtube):