Gelatinous zooplankton abundance and species composition were investigated at 3-h intervals for a 48-h period at a fringing reef in Malaysia. A total of 20 gelatinous zooplankton species were observed; the community was dominated by the calycophoran siphonophore Diphyes chamissonis (79.9%), followed by the trachymedusdae Aglaura hemistoma (5.6%) and Liriope tetraphylla (4.8%). The gelatinous zooplankton were not collected in the water column during most of the daytime hours (1200, 1500 and 1800 h) but were common during the night. However, an abrupt peak in abundance was found at 0900 h on the second day. The times of appearance at night were different depending on the species, and the number of species was also different depending on the hour of sampling. Sampling at 3-h intervals over a 48-h period revealed that the temporal variation (or sampling availability) was large in this study. Careful consideration should be given to the sampling variability in handling the gelatinous zooplankton samples in coral reef areas.