Understanding a wider range of genotype-phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1,832 polymorphic EST-based SNPs and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mtDNA clades with an average of 5.8% among-clade sequence divergence. SNPs revealed five major evolutionarily and genetically distinct groups with an overall FST of 0.170 (95% CI 0.105 - 0.254). Evolutionarily distinct groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4 %) and nine loci (0.5%) with significantly low FST values. Valleys of reduced variation of up to 10 Mb in size surrounding divergent outliers were consistent with selective sweeps. The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analyzed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations will be essential to understand the full range of genetic influences on phenotypic variation in this species.