Previous transplantation analysis has identified a sensitive histocompatibility system in the solitary urochordate Styela plicata that obeys genetic transplantation "rules" identical to those of vertebrates. The current study demonstrates that histocompatibility acts to prevent fusion between conspecifics in sedentary aggregations of this species. Pairs of naturally fused individuals were present at low frequencies (0.06%) in natural populations. Comparative transplantation analysis, in which grafts were transferred from fused donors to panels of single (non-paired) recipients, confirmed that such fusion occurs only between individuals of identical histocompatibility tissue type. Ninety-four percent of recipients yielded identical responses to allografts from both members of fused pairs, suggesting that fused individuals expressed concordant histocompatibility tissue types. In contrast, only 69% of hosts receiving allografts from pairs of randomly selected unfused individuals yielded identical responses to both donor tissues. Allozyme analysis confirmed the specificity of this correlation between fusion and shared histocompatibility type. Fused individuals retained distinct genetic identities for electrophoretically resolved loci independent of tissue type. In light of these results, it is argued that the role of histocompatibility systems in preventing fusion may have been a strong selective force in the evolution of allogeneic recognition.