Hydroid assemblages from the shells of 104 live scallops Placopecten magellanicus and 136 cobbles were sampled from 39 sites on heavily dredged commercial scallop grounds in the Bay of Fundy, northwest Atlantic. The scallop shells were considered pseudo-controls, representing undisturbed ‘island habitats’ naturally interspersed amongst the cobbles. Cobbles were expected to represent disturbed habitat. Samples yielded 51 taxa from 24 genera across substrata. The number of taxa was significantly lower on cobbles. Multidimensional scaling plots and statistical analyses on presence-absence data discriminated 2 divergent assemblages consistent with substratum. Cobble assemblages were characterized by Campanularia volubilis, Clytia hemisphaerica and Clytia sp., while those on the live scallop shells were characterized by the small auto-epizoite Calycella syringa and its hosts Sertularia cupressina and Obelia dichotoma. Species discriminating between the substrata are considered substrate generalists. Fishing effort was introduced as a factor in an analysis of similarity and accounted for a significant proportion of the variance within and between substrata, with larger R2 values associated with the cobble assemblages, as expected. Runner-like forms with small, unbranched colonies and medusa life stages were more frequently found on cobbles than on live scallop shells. Assemblage and life history divergence associated with fishing effort, widespread substrate generalism amongst the principle taxa, and observations from other studies suggest that these observed differences could be related to chronic disturbance of cobbles caused by fishing.