Twenty years (1993–2012) of satellite altimetry dataset, through maps of absolute dynamic topography and their derived geostrophic velocities, as well as monthly climatological maps of windstress and windstress-curl have been used to assess the oceanic variability in the western Indian Ocean region (WIO). We have performed a comparative study between the Agulhas Current Large Marine Ecosystem (ACLME) and the Somali Coastal Current Large Marine Ecosystem (SCCLME) during the current time period when significant levels of climate change related variability have been documented. In the WIO region, climate variability, and/or change are impacting the atmospheric and oceanic circulation, e.g: excessive sea surface warming and consequent air-sea heat flux exchanges in the SCCLME; and broadening and weakening of the Agulhas Current, with potential negative implication on Agulhas leakage, in the ACLME. The latter being caused by an acceleration of the mesoscale eddy field in response to changing atmospheric wind forcing conditions. Therefore, eddies need to be properly quantified, characterized and monitored if their contribution on climate is to be assessed. While four hotspot regions of enhanced mesoscale variability have been identified in the combined Agulhas Somali Currents Large Marine Ecosystem (ASCLME), the main focus of this study has been in the ACLME and in the SCCLME. The results suggest that the levels of variability in these two LMEs are controlled by different physical processes: seasonality appears to be important in the SCCLME, but conversely less important in the Agulhas LME. The census conducted on the eddy field revealed that more eddies have been formed in the ACLME than in Somali Coastal Current. The eddy mean properties have shown that the eddies in the ACLME are smaller in diameter, and higher in amplitude than those in the SCCLME. In addition, the eddies in the ACLME are maintained as coherent structures longer; have been more strongly nonlinear; and have propagated longer distances from their origins than those in the SCCLME. These indicate that the eddies in the ACLME have relatively much stronger implication on the overall retention and transport of hydrographic properties (e.g. heat and salt). Therefore, they could have stronger influence on oceanic lateral fluxes and ocean-atmosphere flux exchanges, thus may influence more strongly the environmental conditions (both in the ocean and atmosphere) in the combined ASCLME, than those in the SCCLME. Time-evolution of the eddies mean properties suggests that inter-annual changes, may have influenced the eddy field differently in the ACLME and the SCCLME: moderate correlation r = 0.6, p = 0.05 has been found between time and eddy mean radius in the ACLME, and also r = 0.6, p = 0.05 was found between time and EKE in the SCCLME. Therefore, eddy size (for the Agulhas LME) and energy content (for Somali LME) could serve as potential indicators of change in oceanographic conditions over time in these LMEs.