Habitats of flatfishes are ordinarily characterized on the basis of depth, sediment type, and temperature. However, features of the benthic environment such as structures created by sessile organisms and different bedforms may also influence habitat suitability. In this investigation, we tested the hypothesis that habitat choices made by juveniles of two economically important flatfishes, Pacific halibut ( Hippoglossus stenolepis Schmidt) and northern rock sole ( Lepidopsetta polyxystra Orr and Matarese), are influenced by structures on the sea floor. In the laboratory, age-0 individuals of both species demonstrated high positive selectivity for habitats with structure (natural sponges, bryozoan mimics, bivalve shells, and sand waves) over smooth sand substratum. The degree of choice was influenced significantly by density of structures, particularly sponges. Small halibut (48–77 and 90–144 mm) were more selective than larger juveniles (270–337 mm), and in sponge habitat juvenile halibut were more selective than comparably sized rock sole. Preference for habitat with structure increased significantly with increasing light level, suggesting that choices were made partially on the basis of visual cues or as related to perceived threat. However, the preference for structured habitat was maintained in darkness. Beam trawl collections made in a flatfish nursery ground near Kodiak, Alaska, revealed that the abundances of age-0 Pacific halibut and rock sole were closely correlated with amounts of shell and echinoderm bycatch in the tows, corroborating the laboratory observations of affinity for habitat structure. Strong preferences for structured habitat in young halibut and rock sole indicate the importance of benthic structures that are frequently removed by fishing gear.