A new genus and species of marine dinoflagellate from the open western equatorial Pacific Ocean, Gynogonadinium aequatoriale gen. et nov. sp., is described from light and scanning electron micrographs. This laterally compressed unarmoured taxon had a triangular cell body in lateral view with two different elongate extensions. The end of the apical extension was spherical with a groove that arises from the epicone in the ventral side of the cell. The antapical extension was longer. The dorsal part of the cingulum showed undulated lists in each margin. The nucleus was ellipsoidal and perpendicularly crossed the cingulum. Dimensions of cells were 90-110 μm long and 43-55 μm wide in lateral view at the level of the cingulum. Gynogonadinium is placed in the order Gymnodiniales, family uncertain.