A comparative investigation is made, for the first time, of direct (ion-composition measurements) and indirect (from topside ion density profiles) methods to determine the O+/light-ion transition height over equatorial latitudes. The transition height determined from the ion-composition follows similar latitudinal and local time variations as the underlying Equatorial Ionization Anomaly (EIA) in the F-region ionosphere. The north-south hemispheric asymmetries in the transition height from ion composition are consistent with the summer-to-winter interhemispheric neutral wind patterns. On the other hand, the transition height derived from ion density profiles is chiefly influenced by changes in the scale height (shape) due to vertical E × B drift at the equator and steep vertical ion density gradients in topside ionosphere. As a result, the transition height derived from topside profiles are systematically lower and exhibit inconsistent latitudinal and local time variations when compared to direct ion-composition measurements at equatorial latitudes.