Capelin (Mallotus villosus (Müller, 1776)), a focal forage fish in the north Atlantic, spawn on both beach and demersal (deep-water) sites throughout their circumpolar distribution. Although these habitats rarely occur in close proximity, demersal spawning sites within 4 km of beach spawning sites (subtidal) have recently been discovered in two coastal embayments in Newfoundland, Canada. The physical environment differs considerably between beach and subtidal spawning sites, creating the potential for local adaptation and genetic divergence of capelin from the two habitats, but this has never been investigated on a fine spatial scale. We use eight microsatellite loci to test for genetic divergence between capelin spawning at beach and subtidal sites within these two coastal regions in Newfoundland. We found no genetic differentiation between fish spawning at beach and subtidal sites or between the two regions. The results from this fine-scale study are in agreement with the lack of habitat-based structure reported in other studies examining beach and demersal sites separated by a larger geographic area. We suggest that instead of showing site fidelity and local adaptation, the facultative use of alternate spawning habitats may be a more successful strategy in an unpredictable environment.