Previous studies have shown that two guilds of predators maintain a discrete morphological polymorphism in the cladoceran Bosmina longirostris in Union Bay, Washington. However, the origin of this polymorphism has remained obscure. The present study shows that the littoral (short-featured) and pelagic (long-featured) forms of this population express nonoverlapping electrophoretic phenotypes at the Pgi locus. Because this correlation between body feature length and Pgi pattern also holds outside of Union Bay, speciation appears to have taken place in the distant past. Bosmina population structure is also examined over space and time. The long-and short-featured populations do not present the intrapopulation heterogeneity described for D. magna elsewhere.