We used a generalized linear model (GLM) to investigate environmental characteristics of capture sites of the invasive small Indian mongoose (Herpestes auropunctatus) on Amami Island, Japan. Data were collected from 2002 to 2011, from an area with the lowest mongoose density. Data on capture levels and environmental factors were obtained within 1 x 1 km grid cells. In addition, we developed an evaluation map that predicts the occurrence of mongooses throughout the island by extrapolating the 2011 results, in which the last mongoose appearance was confirmed. We found that environmental characteristics of capture sites drastically changed during the final stage of the eradication project. From 2002 to 2010, mongooses were captured in grid cells with many gentle ridges. In 2011, when mongoose density became exceedingly low, mongooses seem to have survived in the grid cells with abundant steep ridges, where it was difficult to establish traps. Therefore, environmental factors affected capture levels and the density of the mongoose population. The evaluation map predicts that mongooses could survive on the southwest and southeast island peninsulas. This evaluation map will be helpful in allocating limited labor and financial resources toward the most effective capture strategies. This study suggests that an analysis of pest management data is an important step in the eradication of mongooses. Our results can contribute to long-term projects in invasive pest management not only for the mongoose population on Amami Island, but also for other invasive species globally.