Using Taiwanese longline fishery data, this study investigated the influence of climate variability and environmental conditions in the Indian Ocean on the catch rates and distribution of immature and mature cohorts of yellowfin tuna. The variations in the seasonal distribution of immature and mature cohorts suggest that yellowfin tuna move extensively from the Arabian Sea and Bay of Bengal to the coastal waters of Somalia and around Madagascar in the Indian Ocean. The high recruitments of the immature cohort were found in 1998–2002, and the catch rate of the immature and mature cohorts revealed positive associations with periodicities of approximately 3–4 years. We found that the distributions and catch rates of the two cohorts were sensitive to variations in climatic and marine environments. Sea surface temperature was the most influential environmental variable for both cohorts, and Chl-a was not statistically significant for the immature cohort. There was a significant negative correlation between the catch rate of the immature and mature cohort and Indian Ocean Dipoles (IODs), with periodicities of approximately 3 years during the study period, and had periodicities of approximately 1–3 years with El Niño/Southern Oscillation (ENSO) events. Furthermore, the influence of IODs exhibited greater variance than that of ENSO events, and the influence of ENSO was only evident near the Arabian Sea. The influence of concurrent positive IOD and El Niño events led to lower catch rates for the mature cohort in 2008–2009 in the northwestern Indian Ocean.