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According to tradition the name of the monastery comes from an icon of Mother Mary found under a thyme bush and has been a sacred site for the residents of Sfakia.

The catholicon (main church) of the monastery is a two-aisled church dedicated to the Nativity of Mother Mary (Gennisis tis Theotokou) and the Holy Trinity (Agia Triada), with murals dating back to the Venetian rule period. Many consider it the ‘Agia Lavra of Crete’, since this is where the Liberation Revolution was declared in 1821, just like the mainland one was declared in Agia Lavra Monastery in Peloponnesus. This is why there is an annual mass and commemorative event held on the last Sunday of May at Panagia Thymiani.