The medusa, Aurelia aurita (Scyphozoa, Cnidaria), is considered to be a cosmopolitan species with a worldwide distribution in most seas from the poles to the tropics. Cnidarian is thought to possess two tissue layers: endoderm (gastroderm) and ectoderm, which are separated by huge mesoglea in medusa. The basic morphology of medusa is similar in different populations. Previously we have determined a new protein "mesoglein" as one of the main components of mesoglea. Deduced amino acid sequence of mesoglein contains Zona Pellucida (ZP) domain. In this paper, we have comparied of mesoglein and its gene in medusa from three habitats (White Sea (WsA), Black Sea (BsA), Japonic Sea (JsA)). The set of the mesoglea protein bands after SDS-PAGE is similar in all samples. Nevertheless, JsA mesogleins' M(r) is 53-55 kDa, while WsA and BsA mesogleins have M(r) of 47 kDa. Antibodies raised against WsA mesoglein recognize only mesogleins with M(r) of 47 kDa, but not 53-55 kDa, both on immunoblot and immunocytochemistry. Mesogleal cells and elastic fibrils are stained intensively in the mesoglea both from WsA and BsA but not from JsA. The possibility of gene divergency was checked by PCR with primers specific for WsA mesoglein gene. PCR products of expected length obtained on polyA-cDNA template from mesogleal cells of WsA and BsA medusa but not on cDNA of JsA medusa. Our results evidence that there are two different species in genus Aurelia: Aurelia aurita inhabits White and Black Seas while Aurelia sp. inhabits Japonic Sea. This is consistent with findings of other recept molecular biological studies.