Earlier studies of population dynamics and population genetics of an estuarine amphipod (Stanhope & Levings, 1985;Stanhope, 1989), have suggested that amphipods residing in each of three separate and distinct habitat types within the same estuary exhibited strong habitat fidelity. These populations were separated by as little as 200 m of intertidal mud flat. Laboratory choice tests involving members of each population and the substrate that characterized each habitat type, demonstrated that the members of the two immediately sympatric populations (called Fucus and wood debris) exhibited strong substrate preference for their native habitat type. The third population (bank) showed a strong avoidance for a key feature of one of the habitats (Fucus) and a slight tendency to avoid the other (wood debris). Interpopulation hybrids between wood debris and bank amphipods revealed a highly significant dominance deviation in the F1, towards wood debris preference, which disappeared in the F,. Similarly, F1 generations of crosses between Fucus and bank showed a highly significant deviation towards Fucus preference that was lost in the F2. Crosses between Fucus and wood debris amphipods showed no significant preference for either substrate in the F1 or F2. The results of the interpopulation crosses are interpreted as evidence for polygenic control of habitat preference with dominant genetic effects in wood debris and Fucus amphipods for their native substrate. Knowledge of when and how the wood debris arose, the nature of the original environment, as well as the ancestry of the wood debris population, provide information on shifts in habitat preference in this estuarine invertebrate and suggest habitat fidelity has been a contributing factor in sympatric population subdivision.