Background: Anal cancer comprises only 2.5% of all digestive system malignancies in the United States; only 8200 new cases are diagnosed annually, nevertheless, an increasing incidence rate has been noted. The goal of this study is to describe the incidence rates of anal cancer in New Mexico. New Mexico is a unique, mainly rural state, with unique demographics consisting of a large mix of patients being primarily Non-Hispanic White, Hispanics or Native Americans. Methods: All incident cases of anal cancer diagnosed among New Mexico residents during the twenty-year period 1995-2014 were identified from the population-based New Mexico Tumor Registry. Average annual age-adjusted incidence rates (US 2000 standard) were calculated by the direct method for non-Hispanic whites, Hispanics and American Indians. Incidence rates for non-Hispanic whites in nine core areas of the National Cancer Institute’s Surveillance, Epidemiology, and End Results (SEER) Program served as the comparison. Results: A total of 556 anal cancers were diagnosed among New Mexico residents during the study period, an average of approximate 28 cancers annually. Anal cancer incidence rates per 100,000 were highest for non-Hispanic whites (1.80, 95% Confidence Interval (CI) 1.62-1.98) in New Mexico, which were similar to rates for non-Hispanic whites (1.70, 95% CI 1.66-1.74) in nine core areas of the SEER Program. Statistically significant lower rates were observed in New Mexico Hispanics (0.92, 95% CI 0.76-1.11) and American Indians (0.75, 95% CI 0.45-1.16). Females had higher rates than males in each of these three racial/ethnic groups. Incidence rates increased from 1995-2004 to 2005-2014 for all race/ethnic groups, with the largest increase observed in Hispanic females. Conclusions: Anal cancer incidence rates vary by race/ethnicity and sex in New Mexico. Further research is needed to characterize time trends in incidence and to identify factors that may account for observed differences in incidence rates by race/ethnicity and sex in New Mexico.