ABSTRACT: No-take marine reserves (NTMRs) are advocated as tools to enhance or maintain density and assemblage structure of coral reef fishes. These reef fish population and assemblage attributes may be affected by both NTMR protection and benthic habitat change. Before-after-control-impact-pair (BACIP) sampling designs and long-term (8-30 yr) monitoring at 4 Philippine NTMRs were used to examine the relative effects of NTMR protection and benthic habitat change on densities and assemblage structures of fishery-targeted (Lethrinidae and Lutjanidae) and non-targeted (Pomacentridae) reef fishes. Targeted fish density increased significantly in NTMRs relative to fished control sites at all reserves over time. Non-targeted fish density and hard coral cover displayed a variety of patterns of change over time (unrelated to NTMR protection), but closely mirrored each other. Targeted fish were considered potential predators of non-targeted fish. Availability of potential prey for predators had a larger influence than the effect of potential predators on prey, with both processes much weaker than effects of habitat change. Multivariate analyses of long-term temporal data indicated that 65.8% of the variance in assemblage structure of non-targeted pomacentrids was explained by benthic habitat variables (structural complexity, cover of dead substrate) whereas NTMR protection alone explained only 9.7%. In contrast, 36.2% of assemblage structure of targeted lethrinids/lutjanids was explained by duration of NTMR protection (42.2% excluding effects of typhoons at one reserve), with habitat variables alone explaining 24.7%. These results help clarify the relative effects of NTMR protection, benthic habitat change, and potential trophic interactions on reef fishes targeted and non-targeted by fishing.