Temporal and spatial variability of prevalence of the fungal disease aspergillosis (ASP) affecting Gorgonia ventalina colonies was assessed at several reef sites in La Parguera, southwest Puerto Rico. During 2005 and 2006, all G. ventalina colonies were checked for signs of ASP twice a year, within permanent 20 m² (10×2m) band transects at each of six sites located in three reef zones. Overall, there was high variability in disease prevalence in both space and time (0–28%). The average prevalence of ASP increased significantly from 5.1 ± 9.5% in March 2005 to 14.4 ± 16.0% in September 2006. There was no consistent temporal trend in ASP prevalence affecting all reefs, but shelf-edge reefs had significantly lower prevalence than inner and/or mid-shelf reefs in all sampling periods. Higher disease prevalence found in shallower areas may be related to higher water temperatures in these habitats, and unseasonably high temperatures during the winter and spring of 2006 associated with the extensive bleaching event of 2005.