North Sumatra's Lake Toba is a famous example of a supervolcano caldera, being the world's deepest and largest crater lake. It has been originated since the massive Toba eruption of 74,000 years ago that coincides with global environmental shifts and a significant bottleneck in the global human population. While the freshwater fauna of this lake does not share high levels of endemism, there isCorbicula tobae, an Asian clam species that was described as a taxon endemic to Lake Toba. Here we confirm the validity of this species using morphological, anatomical, and DNA-based evidences, although the general species-level concept for this genus is yet to be developed. Additionally,Corbicula leana, a widespread invasive species, was recorded from Lake Toba for the first time. These two species living in sympatry in Lake Toba appear to exploit different ecological niches within the lake.