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Conservation breeding programmes have become widespread as natural habitats shrink, and have been historically managed using pedigree data and an assumption that population founders are unrelated. Molecular genotyping is able to determine founder relatedness, but is rarely used. To empirically test the impact of assuming founders to be unrelated, we utilized data from 203 founding individuals and 11 subsequent years of breeding records for the Tasmanian devil (Sarcophilus harrisii) insurance population. We integrated molecular data (N = 119 founders) and detailed trapping information (N = 203 founders) to test how founder relationship assumptions impacted the genetic characteristics of the population over time (N = 942 unique individuals). We developed a method to combine molecular kinship (using the TrioML estimator), year of birth and trapping location, and integrated the resulting empirical kinship estimates into population management software. We tested the effect of using pedigree data only, versus our integrated approach, on population outcomes. Inbreeding coefficients evaluated using the integrated approach were significantly higher than pedigree‐only inbreeding coefficients in the first few years following population establishment. A geographic distance‐only approach showed an association between kinship and probability of successful breeding. Our results show the value in using field and/or molecular data combined with pedigree data in conservation breeding programmes to provide new information for managing crucial populations and improving their success. We caution population managers against commencing expensive conservation breeding programmes in the absence of understanding founder relatedness, especially when wild augmentation is a goal. Long‐term costs of assuming founders are unrelated include financial costs, reduced productivity and release of potentially highly inbred individuals. [ABSTRACT FROM AUTHOR]