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For captive breeding to play a significant role in conservation, ex situ populations must be scientifically managed to meet objective goals for retaining representative genetic variation. Imperfect genealogical information requires fundamental assumptions to be made that may bias downstream measures of genetic importance, upon which management decisions are based. The impacts of such assumptions are most pronounced within breeding programmes characterized by a high proportion of individuals of unknown ancestry, as exemplified by the large captive population of the St Vincent parrot (Amazona guildingii). The degree to which microsatellite‐based estimates of relatedness may improve upon the assumptions of conventional pedigree‐based management was investigated using genotypic data collected at eight microsatellite loci and two marker‐based relatedness estimators. The measure, r_xyLR, was …