The MUC family of mucins consists of secreted and membrane-bound forms. Overexpression of the membrane-bound family members, MUC1 (CA15-3), MUC4 and MUC16 (CA125), is found in diverse human carcinomas. However, despite being classified in the same family, little is known about the genetic origins of the carcinoma-associated mucins. The present results show that MUC1 homologs are restricted to mammalian species. MUC1 has no sequence similarity with the other membrane-bound mucins, except for the presence of a sea urchin sperm protein-enterokinase-agrin (SEA) domain. The results indicate that the MUC1 SEA domain originated from heparin sulfate proteoglycan of basement membrane (HSPG2; perlecan), an inducer of tumor cell growth. MUC4 has no SEA domain, but does have (i) a NIDO domain that evolved from an ancestor common to nidogen, and (ii) AMOP and VWD domains that originated from an ancestor common to the Sushi-domain containing protein. MUC16 contains multiple SEA domains that are found in a chicken gene and were subsequently repeated through duplication events. The SEA domains in MUC16 appear to have evolved from agrin before the divergence of birds and mammals. These findings indicate that MUC1, MUC4 and MUC16 evolved from distinct ancestors and that the membrane-bound mucins consist of different subgroups based on their genetic backgrounds.