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The endangered Wild Camel (Camelus ferus Mongolian: хавтгай, khavtgai; Chinese: 野骆驼, ye luo tuo) is the only extant wild species of the Camelini tribe. Surviving only in remote areas of the Gobi deserts of Mongolia and China, this species is threatened with extinction through climate change, associated habitat disruptions and small population impacts. The Wild Camel can hybridize with domestic Bactrian Camel (Camelus bactrianus), and although this introgression has been considered a threat to species survival, the extent to which it has occurred is unknown. DNA was extracted from 257 individuals, from predominantly non‐invasive samples, collected across the in situ and ex situ Wild Camel populations in Mongolia. Genotyping with nuclear markers combined with mitochondrial DNA sequencing was used to gain a greater understanding of the extent and source of introgression and levels of genetic diversity in these populations. Results show evidence of nuclear, mitochondrial, and historic introgression of Bactrian Camel genes in the Wild Camel population in situ, and in some Wild Camel individuals within the ex situ herd. Nuclear introgression was detected between 10% and 22% of the in situ population in Mongolia. Mitochondrial and nuclear DNA analysis have allowed for the sources of introgression to be understood, with paternal introgression being the major source in both in situ and ex situ populations. Results have also shown reduced heterozygosity and elevated inbreeding in the in situ population and reveal similar characteristics in the ex situ herd. Although hybridization is often considered a threat, it may also be an opportunity for species' population viability, and this dilemma creates challenges in conservation management. Whilst the global conservation community currently adopts largely arbitrary thresholds for what is an acceptable level of introgression, a detailed genetic perspective is crucial in understanding hybridization and its effect on conservation. Using non‐invasive nuclear and mitochondrial analysis, this study reveals evidence of introgression in critically endangered Wild Camels (Camelus ferus) from the domestic Bactrian camel (Camelus bactrianus), alongside reduced genetic diversity and higher inbreeding in both in situ and ex situ populations in Mongolia. These findings highlight the need for detailed genetic assessments to guide conservation decisions, as current thresholds for acceptable introgression remain largely arbitrary.