This dataset concerns marine species from six coasts awarded with a Blue Flag from northern Crete, Greece, Eastern Mediterranean. It includes species of benthic and pelagic mega- and macro-fauna and flora. Visual census and photo-identification were applied as non-invasive recording methods. This resource was created within the INTERREG V-A Greece - Cyprus 2014-2020 project "SocioCoast" co-funded by the European Union (ERDF) and national funds of Greece and Cyprus under the grant agreement No 5050709.