Estimates of inbreeding and relatedness are commonly calculated using molecular markers, although the accuracy of such estimates has been questioned. As a further complication, in many situations, such estimates are required in populations with reduced genetic diversity, which is likely to affect their accuracy. We investigated the correlation between microsatellite- and pedigree-based coefficients of inbreeding and relatedness in laboratory populations of Drosophila melanogaster that had passed through bottlenecks to manipulate their genetic diversity. We also used simulations to predict expected correlations between marker- and pedigree-based estimates and to investigate the influence of linkage between loci and null alleles. Our empirical data showed lower correlations between marker- and pedigree-based estimates in our control (nonbottleneck) population than were predicted by our simulations or those found in similar studies. Correlations were weaker in bottleneck populations, confirming that extreme reductions in diversity can compromise the ability of molecular estimates to detect recent inbreeding events. However, this result was highly dependent on the strength of the bottleneck and we did not observe or predict any reduction in correlations in our population that went through a relatively severe bottleneck of N = 10 for one generation. Our results are therefore encouraging, as molecular estimates appeared robust to quite severe reductions in genetic diversity. It should also be remembered that pedigree-based estimates may not capture realized identity-by-decent and that marker-based estimates may actually be more useful in certain situations.