Habitat fragmentation reduces gene flow between isolated populations, thus increasing the risk of extinction through reduced genetic diversity due to the possibility of inbreeding and genetic drift. Ambystomatid salamanders are known to have limited vagility and high breeding site fidelity, potentially making them especially prone to negative effects of fragmentation. We compared gene flow between two populations of Marbled Salamanders (Ambystoma opacum) that are separated by railroad tracks. We additionally compared the genetic diversity of one population across two consecutive years. Observed heterozygosities within sites (0.60-0.65) were significantly lower than expected from the Hardy Weinberg Equilibrium, indicating that the populations may be inbred. F-st values and assignment test results corroborated the interpretation of semi-isolated populations. There was a greater difference in pairwise F-st between the populations on either side of the railroad tracks than between years on one side of the tracks. Assignment tests showed that > 60% of individuals were assigned as residents with high likelihood; whereas, only two individuals at each site were identified as immigrants. Our data suggest that the railroad track may act as a barrier to gene flow in these two populations.