Selective differences among environments rely on isolation or selection coefficients that exceed migration, thus in a highly connect environment there is little expectation of genetic divergence among habitats. The teleost fish Fundulus heteroclitus lives in Spartina saltmarshes along the eastern coast of North America where the tide flushes and then drains these saltmarshes, typical of a well mixed population. The natural history supports this supposition: these fish have small home range of 36m and they reproduce in a common part of the saltmarsh, laying their eggs at the highest tides in the upper tidal regions in mussel shells or among leaves of Spartina alterniflora. Yet, within a single marsh are three microhabitats: 1) tidal basins, 2) intertidal creeks, and 3) tidal ponds, that have meaningful environmental differences in their daily maximum temperatures and oxygen concentration. Based on mark-recapture studies, individuals are often associated with a single habitat. These environmental differences and site fidelity could select for different genotypes. To examine any microhabitat differences in genotypes, individuals from the 3 different microhabitat types from 3 replicate saltmarsh populations along the New Jersey Coast (Mantoloking, Rutgers Field Station, and Stone Harbor) were genotyped at more than 4,000 SNPs using genotyping-by-sequencing (GBS). GBS identified between 2.2-4.4% of single nucleotide polymorphisms (SNPs) with significant outlier FST values between microhabitats of resident fish (p-value < 0.01, FDR = 1%). These SNPs may be adaptively important, and suggest that selection is surprisingly effective in altering allele frequencies over very small geographical distances.