Hybrid cetaceans occur in both captive and natural environments. This study is the first to describe the external morphological and genetic characterizations of natural intrageneric hybridization between the common bottlenose dolphin, Tursiops truncatus, and the Indo-Pacific bottlenose dolphin, T. aduncus, in Japanese waters. In November 2019, a stray dolphin was seen in Moriura Bay, Wakayama, Japan, and was a male that measured 241.5 cm in body length in July 2020, after an incidental catch in February 2020. Moderate speckles in the genital area of the dolphin were observed, which is a characteristic of T. aduncus. The dolphin had 22–23 pairs of teeth in each jaw, a quantity consistent for both species. The length of the rostrum and the size of flippers were within the range of T. aduncus. The mitochondrial DNA D-loop region haplotype was 99% homology with those from T. aduncus found in Chinese and Japanese waters. Microsatellite analysis revealed that the dolphin contained ratios of approximately 50% of both T. truncatus and T. aduncus lineages; the dolphin could therefore be an F1 hybrid between a female T. aduncus and a male T. truncatus. Further genetic studies are required to elucidate the origin of this hybrid dolphin.