A remarkable new species of the subgenus Japonigekko from the islands of Gotō Nada and offshore islands of Kagoshima Prefecture, Kyushu, Japan, inhabiting rocky coastal habitats, is described based on morphological characters and molecular evidence. Morphologically, Gekko (Japonigekko) asahi sp. nov. can be distinguished from its congeners by its moderate body size; interorbital scales between anterior corners of eyes 34–44; dorsal tubercles large, strongly elevated, and arranged in 12–16 rows at midbody; 127–158 midbody scale rows; 32–45 ventral scale rows; 158–189 ventral scales between the mental and the cloacal slit; subdigital lamellae 8–11 on finger I, 9–14 on finger IV, 9–12 on toe I, and 10–18 on toe IV; webbing absent; 6–9 precloacal pores in males, and absent in females; one postcloacal tubercle on each side, with the midpoint of the tubercle distinctly concave in some male individuals; and its distinctive dorsal coloration. Phylogenetically, the new species represents a distinct clade within the subgenus Japonigekko, forming a sister group with G. kaiyai from Henan Province of China, and together they cluster with G. hokouensis. It differs from its congeners by uncorrected p-distances of at least 15.1% in ND2 and 7.6% in 16S. Currently, the new species is known only from low-elevation coastal rocky shores and building walls on island of Gotō Nada and Nishisonogi Peninsula, Nagasaki Prefecture and offshore islands of Kagoshima and Satsuma Peninsula, Kagoshima Prefecture, Japan. The discovery of this new species increases the total number of species in the subgenus Japonigekko to 40, of which seven species are distributed in Japan.