Loss of genetic variation through genetic drift can reduce population viability. However, relatively little is known about loss of variation caused by the combination of fluctuating population size and variance in reproductive success in age structured populations. We built an individual-based computer simulation model to examine how actual culling and hunting strategies influence the effective population size (Ne) and allelic diversity in Yellowstone bison over 200 years (∼28 generations). The Ne for simulated populations ranged from 746 in stable populations of size 2000 up to 1165 in fluctuating populations whose census size fluctuates between 3000 and 3500 individuals. Simulations suggested that ∼93% of allelic diversity, for loci with five alleles will be maintained over 200 years if the population census size remains well above ∼2000 bison (and if variance in male reproductive success is high). However for loci with 20 alleles, only 83% of allelic diversity will be maintained over 200 years. Removal of only juveniles (calves and yearlings) resulted in longer generation intervals which led to higher maintenance of allelic diversity (96%) after 200 years compared to the culling of adults (94%) when the mean census size was 3250 (for loci with five alleles). These simulations suggest that fluctuations in population census size do not necessarily accelerate the loss of genetic variation, at least for the relatively large census size and growing populations such as in Yellowstone bison. They also suggest that the conservation of high allelic diversity (>95%) at loci with many alleles (e.g., ⩾5) will require maintenance of a populations size greater than approximately 3250 and removal of mainly or only juveniles.