The abundance and species richness of highly social bees (Apinae: Meliponini, Apini) were studied at 12 dipterocarp forest sites in Sabah, northern Borneo, using standardized honey-water baiting assays. The 12 sites were grouped in five localities varying in the degree and history of disturbance from selective logging. A baiting assay consisted of spraying diluted honey on vegetation along transects and recording bee arrival on the same day. Repeated assays of the same sites were run in two consecutive years, 1998 and 1999. One-way repeated-measures ANOVAs were calculated on bee abundance and species richness, with locality and year as independent factors. There were significant or marginally significant effects of forest locality on all measures of bee abundance and species richness. However, there were also significant interactions between year and locality on these variables, thwarting conclusions on the effects of logging on bee communities. The diverging results of the two years are likely related to spatio-temporal variation of flowering activity prior to and during the assays, with between-year differences being amplified by pronounced differences in climatic conditions (ENSO). Local or regional differences in flowering phenology complicate the application of resource-based baiting techniques for between-site comparisons of bee diversity.