Percentage cover of coral reef associated algae increased significantly from 2003 to 2007 at two shelf edge sites in southwest Puerto Rico (42.8 % to 75.3% at Weinberg Reef and 67.4% to 81.8% at El Hoyo). While the increase was driven largely by increase in cover of Lobophora variegata, percent cover of the individual spatially dominant algal species was highly variable temporally. The variability was apparent even at the subquadrat level (0.0625m²) for which adjacent subquadrats demonstrated little concordance in species cover over subsequent sampling periods.