Beaked whales represent around 25% of known extant cetacean species, yet they are the least known of all marine mammals. Identification of many Mesoplodon species has relied on examination of a few stranded individuals. Particularly, the ginkgo-toothed beaked whale (Mesoplodon ginkgodens) and Deraniyagala's beaked whale (Mesoplodon hotaula) are among the least-known of beaked whale species, without confirmed sightings of living individuals to date. We present a sighting of 3 free-ranging individuals of M. ginkgodens/hotaula whale from a dedicated marine mammal vessel survey carried out in the South China Sea in April and May 2019. Photographic data (301 photographs) from the sighting were compared to photos of fresh stranded ginkgo-toothed beaked whale and Deraniyagala's beaked whale from both historical and unpublished records. We found that free-ranging M. ginkgodens and M. hotaula individuals can be easily distinguished from other Mesoplodon species due to differences in melon and gape shapes and coloration patterns. However, accurate at-sea differentiation of M. ginkgodens and M. hotaula may not be possible due to high similarity in both coloration and scarring patterns. In addition to our photo-identification data, we collected what we believe to be the first preliminary descriptions of surfacing behavior and diving patterns of one of these species. Finally, the presence of scars possibly caused by fishing gear or marine litter raises concerns about anthropogenic impacts and conservation of these poorly known species.