We developed a habitat suitability index (HSI) model to identify the optimal habitats of swordfish (Xiphias gladius) in the equatorial Atlantic Ocean. Environmental variables, including sea surface temperature (SST), mixed layer depth (MLD), chlorophyll-a concentrations, and sea surface height anomaly, as well as catch and effort data from Taiwanese longline fisheries, were used. The geometric mean model including all the above environmental variables was identified as the most parsimonious model for yielding HSI predictions coinciding with productive fishing grounds with high fishing effort. Swordfish mainly aggregated in the northwest region during March–May and spread southeast thereafter in response to seasonal shifts in oceanographic conditions. There was annual variation in the distribution of habitat patches, and the habitat quality was reduced in the northwest region of the equatorial Atlantic Ocean during 2005. The apparent spatial shifts in optimal habitats might be linked to reduced MLD and elevation in sea surface height, which might be related to climate variability (e.g. Niño-Southern Oscillation and/or Northern Atlantic Oscillation). Because environmental data regarding climate change scenarios are becoming readily available, we can utilize the proposed HSI models to evaluate possible changes in habitat suitability resulting from climate change and provide scientific advice for the development of management regulations.