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Translocations are a tool widely used by wildlife managers, yet their impact is often insufficiently evaluated. Most translocation studies only assess the initial establishment phase, and the majority of long-term persistence studies to date have only tracked female fecundity. Male genetic integration for mitigative translocations have as of yet not been assessed and could greatly undermine the validity of translocation evaluations. To test for successful male integration, we determined genetic paternity of 92 desert tortoise hatchlings (Gopherus agassizii), from both resident and translocated females, four years after the initial translocation event and found that all 35 hatchlings with a paternal match in our genotype database were sired by residents. Given that translocated males constitute 46% of the genotyped males found in the home ranges of the females, they produce significantly fewer offspring than resident males in the same area (G-test, p value < 0.0001). This is the first study assessing paternal genetic integration following a translocation of a wild sourced population into a native resident population. We hypothesize that male condition following the translocation, female mate preference for prior residents and competitive exclusion by resident males may contribute to the lower reproductive output of translocated males. We advocate the use of genetic paternity testing in other species to determine the generality of male translocation success across taxa given this unexpected and alarming result.