Six coral reefs in southwest Puerto Rico were censused in 1995 to examine species assemblages and their spatial distributions. This census was repeated in 2005 to detect temporal changes in distributions and abundance of species and associated substrata. Ten years after the original study, analyses indicated that 13 species of fishes declined significantly in numbers (a decrease of 21–100%), one species increased by 49% and nine species did not change in abundance. Among invertebrate species, one sponge, two corals and the urchin Diadema all increased in numbers (91–2167%), whereas one coral, a zoanthid, two urchins and three algae all declined significantly (24–70%). Four gorgonian genera did not change in numbers of colonies but grew significantly in size over 10 years. No change in abundance occurred among 14 species of invertebrates and plants. Overall species richness decreased significantly. Substrata sizes, an important habitat characteristic, remained the same on backreefs but changed significantly on forereefs: the amount of boulder decreased by 21% while the smaller substrata (cobble, pebble and sand) increased (85, 382 and 28% respectively). Sea surface temperature was warmer in 2005 than in 1995.