The long-spined sea urchin Diadema antillarum has been the focus of multiple studies since the mass mortality event in the 1980s. The recovery of this key herbivore in the wider Caribbean is essential for the well-being of coral reefs. This study examined the population density and structure of D. antillarum at seven northern fringing reefs of Puerto Rico between 2011 and 2013. The total mean density of the sea urchins in northern Puerto Rico was 0.9 ±0.3 ind m−2. Densities of D. antillarum significantly differed among sites, but not temporally. Differences in mean sizes were significant among sites and seasons. Areas with higher densities of D. antillarum showed lower cover of non-calcareous algae. Wave exposure was correlated with the abundance of the sea urchin. This study indicates that the observed abundance of D. antillarum has not yet returned to pre-mortality levels. However, densities showed some degree of recovery when compared with previous studies, enabling at least some degree of control on fleshy macroalgae communities. No significant changes in density occurred between 2011 and 2013, and sites with higher densities were generally located in leeward areas. The low relative abundance of small size individuals points towards recruitment limitation as an explanation for the limited recovery of D. antillarum.