Mitochondrial and nuclear gene variation is described from populations repr
esenting the range of two species of rare pygmy sunfishes, Elassoma boehlke
i and Elassoma okatie, in the Carolinas. Mitochondrial control region seque
nces provide evidence for a minimum of four Evolutionarily Significant Unit
s (ESU), two each within E, boehlkei and E. okatie. Significant allele freq
uency differences at a single nuclear gene locus corroborate the distinctiv
eness of these ESUs, Phylogenies based on control region haplotypes and fre
quencies of nuclear alleles are inconsistent with the currently described r
ange of E. boehlkei and E. okatie, Despite inconsistency with described spe
cies boundaries, the result of this genetic analysis for rare species manag
ement is clear: conservation strategies that describe distinct population s
egments inhabiting individual river systems should be encouraged.