A population bottleneck is an event in which one population experiences a substantial reduction in number of individuals. The genetic consequences of bottlenecks include increased inbreeding, accelerated rate of random genetic drift, and decreased genetic diversity and adaptive evolution potential. These effects increase extinction probability and raise great concerns in conservation. Most previous theoretical work was developed under a simplifying assumption of discrete generations, thus creating complexities when applying the models to long-lived organisms. This study developed an overlapping-generation model to study the genetic consequence of bottlenecks in long-lived organisms. This model is implemented in a computer simulation program, BottleSim, to serve as a tool to evaluate the genetic consequences of bottlenecks. The first part of this study employs computer simulations to investigate the effects of generation model, longevity, reproductive system, and population size on the rate of decline in genetic diversity. The results suggest that each of these factors has a substantial effect on the rate of decline in genetic diversity during bottlenecks, and the traditional discrete-generation model tends to underestimate the rate. The second part of this study uses microsatellite markers to compare two ornate box turtle (Terrapene ornata) populations, one of which experienced a recent bottleneck due to habitat loss while the other is relatively undisturbed. The heterozygosity excess test detected the genetic signature of a recent bottleneck in the small population, but the bottleneck had little effect on the level of genetic diversity in this case. Based on life history attributes of this species and genetic projections made by computer simulations, a census population size of 700 is required for this imperiled population to maintain 90% of its observed allelic richness in the next 200 years. In conclusion, bottlenecks can have very different genetic effects on long-lived species with overlapping generations and short-lived species with discrete generations. The life history of the organism must therefore be taken into account in practical conservation planning. This study developed a tool to facilitate conservation work involving long-lived species with overlapping generations, identified an imperiled ornate box turtle population, and provided conservation recommendations for this population.