We examined spatially clustered distribution of jumbo flying squid (Dosidicus gigas) in the offshore waters of Peru bounded by 78°–86°W and 8°–20°S under 0.5°×0.5° fishing grid. The study is based on the catch-per-unit-effort (CPUE) and fishing effort from Chinese mainland squid jigging fleet in 2003–2004 and 2006–2013. The data for all years as well as the eight years (excluding El Niño events) were studied to examine the effect of climate variation on the spatial distribution of D. gigas. Five spatial clusters reflecting the spatial distribution were computed using K-means and Getis-Ord Gi* for a detailed comparative study. Our results showed that clusters identified by the two methods were quite different in terms of their spatial patterns, and K-means was not as accurate as Getis-Ord Gi*, as inferred from the agreement degree and receiver operating characteristic. There were more areas of hot and cold spots in years without the impact of El Niño, suggesting that such large-scale climate variations could reduce the clustering level of D. gigas. The catches also showed that warm El Niño conditions and high water temperature were less favorable for D. gigas offshore Peru. The results suggested that the use of K-means is preferable if the aim is to discover the spatial distribution of each sub-region (cluster) of the study area, while Getis-Ord Gi* is preferable if the aim is to identify statistically significant hot spots that may indicate the central fishing ground.