Broom and threadleaf snakeweed reduce rangeland productivity throughout the western United States. These closely related species are only distinguishable at flowering and are highly variable in morphology and phenology. The objective of this study was to evaluate the genetic variation among snakeweed populations from Arizona, New Mexico, Texas, and Wyoming using isozyme analysis. Plants from each population were transplanted into pots and maintained in a greenhouse for 6 mo prior to analysis. Protein was extracted from young leaf tissue and separated using starch gel electrophoresis. Genetic variation was assessed based on expressed isozyme patterns of 10 enzymes. Of 10 enzymes tested, 16 loci were identified. Total genetic diversity (HT) was large for the eight polymorphic loci in broom snakeweed and three polymorphic loci in threadleaf snakeweed. Genetic variation among populations (DST) of both species contributed the major portion of diversity, but diversity among individuals within each population (HS) was also present. Phylogenetic analysis using Nei's genetic identity and distance determined broom snakeweed populations from New Mexico and Texas were more alike than those from Wyoming and Texas, or those from Wyoming and New Mexico. Compared to genetic differences among New Mexico broom snakeweed populations defined in a previous study, genetic diversity was greater among populations from different states. In addition, genetic variation was smaller in threadleaf snakeweed populations relative to broom snakeweed populations. Results concurred with previous research designating broom snakeweed as the progenitor of threadleaf snakeweed. Local populations of each species have probably developed due to long-term environmental selection.