Among sympatric populations of lineages I, III, and VI of Tubifex tubifex, lineage VI recently was shown to exhibit resistance to Myxobolus cerebralis, the causative agent of whirling disease in salmonids. Determining the genetic differentiation exhibited among T. tubifex from different habitats and among lineages is key to understanding the etiology of whirling disease. This study examined genetic divergence within two lineages (III and VI) of T. tubifex from shallow and deep habitats in a tailwater at Navajo Dam in the San Juan River, New Mexico. Starch-gel electrophoresis was used to delineate alleles of T. tubifex from deep and shallow habitats. Cellulose-acetate electrophoreses was used to delineate alleles of lineages III and VI of T. tubifex. Of the seven allozymes analyzed, leucine aminopeptidase (LAP) differentiated between lineages III and VI. The LAP allele ‘A’ was exhibited only within lineage III whereas both alleles ‘A’ and ‘B’ were exhibited within lineage VI. Furthermore, lineages III and VI exhibited a genetic distance of 0.124, but were more similar to each other than to T. tubifex from the Great Lakes. Genetic divergence between lineages III and VI of T. tubifex, when coupled with differences in resistance to M. cerebralis, provide support to the hypothesis that populations of T. tubifex are members of a cryptic-species complex.