Molecular clock
Using mitochondrial DNA, a 2010 phylogenetic analysis reported that the Japanese angelshark forms a clade with the other Asian angelsharks included in the study: the ocellated angelshark ("S. tergocellatoides") and the sister species pair of the Taiwan angelshark ("S. formosa") and the Indonesian angelshark ("S. legnota"). These Asian species are, in turn, allied with European and North African angel shark species. Molecular clock estimation suggested the Japanese angelshark lineage diverged from the rest of the Asian angelsharks some 100 million years ago during the Cretaceous.