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In this study, we for the first time observed two subsurface cyclonic eddies (SCEs) in the southeastern Tropical Indian Ocean. One SCE (SCE‐C) was observed along 8°S transect during the cruise conducted in July 2016. Another SCE (SCE‐A) was also observed near 8°S but by an Argo float in November 2005. The SCE‐C had a maximum thickness of about 500 m (300–800 m) and a radius of ~90 km, while the SCE‐A has a vertical extent of 700 m (200–900 m) and a radius larger than 110 km. The water trapped by SCE shows a three‐compartment structure. Both the two SCEs are characterized by stratified water with negative lens structure and cause prominent temperature/salinity/spiciness anomalies in a wide density range. As the water carried by SCEs is stratified, we can trace the SCE origin by finding an area sharing the same water property with the SCE on different density surfaces. The result suggests that the two SCEs originate from the southwest coast of the Sumatra Island. Considering the topography and hydrologic characteristics of the SCE origin, we speculate that the SCEs are generated due to topography‐induced South Java Undercurrent instability. Subsurface eddies usually have long lifespans and can carry fluid parcels and transport them far away from the eddy origin. However, compared with surface eddies, subsurface eddies are poorly observed because they usually have small or no surface signatures. In this study, we for the first time observed two subsurface cyclonic eddies (SCEs) in the southeastern tropical Indian Ocean. The SCEs were characterized by stratified water with negative lens structure. Further analysis suggested that the SCEs should be generated off southwest coast of the Sumatra Island due to topography‐induced South Java Undercurrent instability and move southwestward. These results provide new insight into the SCEs in the southeastern tropical Indian Ocean. Two subsurface cyclonic eddies are observed in the southeastern Tropical Indian OceanThe subsurface cyclonic eddies are characterized by stratified water and cause prominent water property anomalies in a wide density rangeThe subsurface cyclonic eddies should be generated off southwest coast of the Sumatra due to topography‐induced undercurrent instability