the freshwater invertebrate daphnia can persist in historically metal-contaminated lakes due to its ability to adapt to metal contamination. since different daphnia isolates have been shown to have varying degrees of tolerance to metals, metal toxicity testing in daphnia is a useful model for studying intra-population variation. however, many ecological studies of daphnia use single isolates to represent the population, with an assumption of minimal diversity. copper lc50 tests were performed among daphnia isolates from clean and metalcontaminated lakes in order to analyze variation in metal tolerance. daphnia from metalcontaminated lakes were found to be significantly more tolerant to copper than clean lake isolates (p = 3.5 x 10-4), and had a slightly lower degree of variation of lc50 (cov = 19.9%) compared to that of clean lakes (cov = 21%). however, pairwise lc50 comparisons found more significantly different comparisons in metal-contaminated lakes (40.7%) than clean lakes (25.9%). of the within-lake pairwise lc50 comparisons, 33.3% varied significantly, compared to 65.9% for among-lake comparisons. overall variances within lakes were not significantly different than among lakes (p = 0.147), demonstrating high intra-lake variability in metal tolerance despite significant overall differences in average values. the lactate dehydrogenase gene (ldh) and nadh dehydrogenase 5 gene (nd5) were used to distinguish daphnia pulicaria, daphnia pulex and hybrid species and analyze genetic diversity in metal tolerance. analysis of ldh genotypes revealed that daphnia with s and f alleles were significantly more tolerant than daphnia with two f alleles (p = 1.8 x 10-4). phylogenetic reconstructions based on nd5 gene sequences showed that daphnia isolates from metal contaminated lakes clustered together showing a reduction in genetic diversity, while clean lake isolates clustered among four different haplotypes (three pulex and one pulicaria). these results suggest that metal contamination reduces genetic diversity among daphnia isolates within lakes by selecting for metal-tolerant phenotypes, which correlates with the ldh sf genotype. this reduction in diversity can negatively impact daphnia’s ability to adapt to future environmental stress, and the high variability within the populations from clean lakes suggests multiple isolates should always be used when collecting representative daphnia isolates for studies.