We developed an “Integrated Habitat Index (IHI)” model based on the quantile regression method using survey data collected at 43 sites in waters near the Cook Islands from September, 2012 through November, 2012. The model variables included vertical profile data for temperature, salinity, chlorophyll-, horizontal current, vertical current and catch per unit effort (CPUE) of albacore tuna(), and the interactions among these variables. Models were developed for five 40 m water strata between 40 m and 240 m and the entire water column to predict the spatial distribution of albacore tuna. The environmental variables measured at modeling sites were used as inputs to the IHI models to predict the IHI value of the 5 strata and the entire water column. We tested for a significant difference between the observed CPUE and predicted CPUE within the 5 water strata and the entire water column using a Wilcoxon test. The Spearman correlation coefficients were assumed to indicate the predictive power of the IHI model. The trend line of the arithmetic average about the predicted IHI for the 5 strata was compared with the CPUEs at the specific depth stratum. The environmental variables at validation sites were used to validate the model’s predictive power. These data were input into the CPUE models to predict the CPUE of the 5 water strata and the entire water column. We used a Wilcoxon test to compare between the predicted and observed CPUEs within the 5 water strata and the entire water column to validate the IHI results. The CPUE for albacore tuna in the 5 strata and the entire water column exhibited a skewed normal distribution with a longer left tail. There was no significant difference between the nominal CPUEs and predictive CPUEs of albacore in the 5 water strata and the entire water column at the modelling sites or the validation sites. The IHI models had good predictive power, and were able to accurately predict the distribution of albacore tuna in the 40 strata and in the entire water column. The key environmental parameters in the IHI models differed among the depth strata. In the shallow water (40), there was a close relationship between the CPUE and water color. Conversely, water temperature, sea currents, and bait and water temperature were the most significant variables in the 80, and generally between 160 and 200 m. The CPUE was 20.31 ind/(1000 hooks) in this water strata. The IHIs for albacore tuna in the area between 13°S167°W were relatively high. When fishing in these areas, our results suggest that fishing gear should be deployed at a depth of 160