We used mark-recapture analysis to investigate the dynamics of a black bear (Ursus americanus) population in northern Idaho where food availability varies seasonally and annually. We conducted noninvasive genetic sampling (NGS) during 2003–2006 in the Purcell Mountains of Idaho to collect black bear DNA samples for individual identification of bears. We used a combination of both mark-recapture and genetic analyses to evaluate whether variation in vital rates and genetic substructure was a function of changing food productivity in the study area. We found a heterozygote deficiency and detected genetic substructure within a single year, suggesting we sampled multiple subpopulations (a Wahlund effect). Our mark-recapture analyses suggested this pattern was in response to interannual variation in summer berry abundance. This project demonstrated the potential pitfalls of interpreting mark-recapture data over short time periods without ancillary data that can be used to evaluate mechanisms of population change. We found NGS provided information not only for traditional mark-recapture analysis but also complimentary insights into demography gained through genetic analyses. Combining mark-recapture estimates with analyses of population genetics provides a more complete understanding of population dynamics than either method alone, thus improving ecological inferences and effective management. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.