Specific cell adhesion in the marine sponge Microciona prolifera is mediated by an extracellular aggregation factor complex, whose main protein component, termed MAFp3, is highly polymorphic. We have now identified MAFp4, an approximately 400-kDa protein, from the aggregation factor that is translated from the same mRNA as MAFp3. The existence of multiple potential sites for N-glycosylation and calcium binding suggests a direct involvement of MAFp4 in the species-specific aggregation of sponge cells. The deduced partial polypeptide consists of a 16-fold reiterated motif that shows significant similarity to a repeat in an endoglucanase from the symbiontic bacterium Azorhizobium caulinodans and to the intracellular loop of mammalian Na+-Ca2+ exchangers. Restriction fragment length polymorphism analysis indicated that the genomic variability of MAFp4 is high and comparable to that of MAFp3. Their combined polymorphism correlates with allogeneic responses studied in a population of 23 sponge individuals. Peptide mass fingerprinting of tryptic digests of the polymorphic MAFp3 bands observed on polyacrylamide gels after chemical deglycosylation of the Microciona aggregation factor revealed that the variability detected on Southern blots at least partially reflects the individual variability of aggregation factor protein components. Polyclonal antibodies raised against MAFp3 strongly cross-reacted with a 68-kDa protein localized in sponge cell membranes. Immunohistochemical use of the anti-MAFp3 antibodies strongly stained a cell layer along the line of contact in allogeneic grafts. We show that the transcription level of the MAFp3/MAFp4 mRNA in sponge allo- and isografts is clearly increased in comparison with non-grafted tissue. These data are discussed with respect to a possible evolutionary relationship between cell adhesion and histocompatibility systems.