Earlier and recent sampling carried out in the Aegean Sea revealed the presence of 20 asteroid, 14 ophiuroid, 21 echinoid, and 1 holothuroid species. The ophiuroid Monaphiura apicula, and the echinoids Arbaciella elegans, Echinus melo and Hemiaster expergitus are recorded for the first time in the Eastern Mediterranean; the latter has previously been known only from the Western Mediterranean. The ophiuroid Amphiura (Acrocnida) brachiata is recorded for the first time in the Aegean Sea. For all species, information on their distribution and habitat is given. A checklist of the Mediterranean and Black Sea echinoderms, as well as their distribution in the Mediterranean territorial areas and the Black Sea are also presented. Furthermore, the faunas of the Mediterranean territorial areas are compared. According to the considered data, the number of species decreases as follows: Western Mediterranean, Aegean Sea, Adriatic Sea, Central Mediterranean, Levantine Sea and Black Sea. Species with an Atlanto-Mediterranean distribution dominate in all areas and are followed in numbers by the Mediterranean endemics and cosmopolitans. Four species of Indo-Pacific origin are located in the Levantine and SE Aegean seas.