Canopy ants were surveyed at Stability of Altered Forest Ecosystem, Sabah Malaysia to look for effect of different sizes of forest fragmentation and an El-Nino event. We also surveyed unmanipulated control areas: old growth forest, unfragmented logged forest and oil palm plantation. We found that experimental isolation of 10 ha forest fragments and also salvage logging (matrix habitat) reduced ant abundance, while 1 ha fragments, matrix habitat and control oil palm sites experienced reduced canopy ant species richness. No changes in abundance for any control sites, or for species richness in primary forest and unfragmented logged forest. Ant community composition did not change in any of the habitats. We conclude that, fragments 100 ha or greater support canopy ant communities indistinguishable from those in unfragmented logged forest in terms of canopy ant abundance, species richness and composition. These effects may have been amplified by El Nino, which also resulted in reduction in species richness in the control oil palm habitat, indicating that more degraded habitats may be more vulnerable to extreme climatic events. Ongoing post-fragmentation surveys during non-El Nino years are now needed to tease out the longer-term effects of fragmentation and those of extreme climatic events.