The D2-D3 and ITS regions of rDNA from 33 Florida populations of Belonolaimus spp. were sequenced and subjected to phylogenetic analysis. Our objective was to derive a theoretical evolutionary framework for interpreting phenotypic differences as they relate to the taxonomy of the genus. The most striking aspect of the phylogenetic analysis is that none of the three nominal species (B. longicaudatus, B. euthychilus, and B. gracilis) are monophyletic. Additionally, two taxa appear to have discordant ITS and LSU sequences. Three major clades of B. longicaudatus exhibited discernible, overlapping, geographic foci from east to west across the peninsula. Morphological character states considered important for species identification (stylet:tail ratio > or < unity; absence or presence of lip constriction) were paraphyletic; however, these characters may be valid if different quantitative states are used (e.g., stylet:tail ratio > or < a value somewhat greater than 1.0; degree of lip constriction). We were unable to identify suites of morphological/morphometric character states that discriminated between the molecular-derived clades of B. longicaudatus. The large number of autapomorphies for the relatively conserved D2-D3 region both between and within the nominal species reinforces previous observations that the genus Belonolaimus is far more complex than currently recognized.