Spear squid Loligo bleekeri is widely distributed in the Japanese coastal waters. The fisheries depend largely on four stocks: the southern and northern stocks both in the Japan Sea and the coastal regions of the Pacific. The catch per unit effort (cpue) for the northern stock in the Japan Sea decreased substantially during the 1980s but increased during the 1990s, while the abundance index for the southern stock showed the opposite trend. The cpue for the southern and northern stocks in the Pacific coast showed a similar pattern to that in the Japan Sea. The synchrony in the abundance trends between the Japan Sea and the Pacific Ocean, and latitudinal differences between the northern and southern stocks indicate the impact of the climate regime shift. Generalized additive model analysis identified significant effects of environmental factors. Increased water temperature had a positive effect on the northern stock but a negative effect on the southern stock in the Japan Sea and the Pacific, whereas El Niño–southern oscillation events and the Asian monsoon had additional significant effects on the Pacific stocks. These results suggest that the abundance trends of spear squid were largely forced by environmental factors with latitudinal differences in the response to the climate regime shift.