A biogenic structure ecosystem of extensive worm tubes of Chaetopterus sp. harbouring different fish species was investigated at Anacapa Island, southern California to determine the numerical abundance, species composition, body size, and seasonality of the ichthyofauna associated, and their relation with the worm patch size. Bimonthly, a 30-m swimming transect and a quadrat-based survey estimated the length of each fish, the type of habitat it occupied, and the worm tube patch size-class. Larger worm mats harboured higher densities of fish, mainly the dominants Rhinogobiops nicholsii and Chaenopsis alepidota, which live inside the worm tube patches. Fish population density varied between the ‘inside’ and ‘edge’ of Chaetopterus beds as smaller and younger individuals were hindered from reaching the middle of the patch by larger, older and territorial individuals. The prevalence of positive and significant correlations between the abundance of smaller individuals of R. nicholsii and specific habitat features (e.g. edge) suggests that the abundance and distribution of juveniles might be habitat-dependent besides intraspecific competition between older and younger individuals. There was a decreasing density of R. nicholsii at greater than 20 cm away from worm tubes and there were no individuals beyond 6 m away from structure. Chaenopsis alepidota was not recorded when the patch size was less than 50% tube coverage. Our results revealed that complex habitat structure had a positive influence on the abundance of juvenile and adult of C. alepidota and R. nicholsii, and suggest that these structured areas are preferentially utilized, which contributes to its patchy distribution pattern. The presence of biological structures in low-relief sedimentary habitats can have critical functional significance even for reef fish. These important habitat features may need to be identified and protected.