The genus Philonotis is generally considered taxonomically difficult because of high levels of phenotypic variation and frequent intergradation between species. Philonotis fontana and P. caespitosa, two poorly understood taxa that appear to be widespread across Europe and North America, are difficult to distinguish and some authors consider them two varieties of one species or even synonyms. Isozyme variation at 13 putative loci among 22 European samples representing these two species indicates that the two taxa are genetically distinct although closely related (Nei's genetic identity = 0.84). In a second part of the study, ten individuals were sampled from each of four populations from the Czech Republic; one population was clearly P. fontana (based on morphology), one was P. caespitosa, and two populations were morphologically aberrant and could not easily be assigned to one species or the other. This second study tested alternative hypotheses that the intermediate phenotypes reflect morphological plasticity, or that they result from interspecific hybridization. The results corroborate genetic differences between P. fontana and P. caespitosa, but the two morphologically aberrant populations contained alleles from both species. Plants in one of the morphologically aberrant populations were more distinct genetically from both P. caespitosa and P. fontana than were the two species from one another. The other morphologically aberrant population could be viewed as either intermediate between the two species in terms of its isozymes, or it could be included in a broadly circumscribed P. caespitosa. The results are consistent with interspecific hybridization, although phenotypic plasticity probably also contributes to morphological variation.