Settlement and metamorphosis of many benthic invertebrate larvae are dependent on detection of cues from biofilm bacteria. The identity of the cues that mediate these interactions remain largely unknown. However, the same bacterial genera are repeatedly implicated in this induction across many different phyla. Earlier studies had shown that larvae of the coral Pocillopora damicornis were sensitive to strain differences in single bacterial species. To better understand bacterial cueing specificity, we exposed larvae of the serpulid polychaete Hydroides elegans and the sponge Haliclona caerulea to monospecific biofilms from multiple strains of the two bacterial species: Pseudoalteromonas luteoviolacea (4 strains) and Thalassotalea euphilliae (3 strains) isolated from inner harbor or coral reef environments. We found that larvae of H. elegans and H. caerulea, both biofouling species typical of harbors, had stronger responses to the harbor strains of bacteria. The three strains of T. euphilliae, all isolated from a coral reef, had different inducing effects for P. damicornis and H. elegans: each animal was induced to metamorphose by a different strain. Interestingly, the different strains of P. luteoviolacea also exhibited differences in the amount of violacein they produced, with the coral reef strain producing significantly higher levels of the characteristic secondary metabolite. Marine biofilm bacteria rapidly colonize new surfaces and show community-compositions that differ between habitats. We hypothesize that small, strain-specific differences in bacteria are detected by larvae of marine invertebrates to determine the suitability of a habitat for recruitment.