Species-specific genomic information has the potential to transform modern conservation management strategies through improved genomic impact assessment and management outcomes. Gaining genomic insights into genetic diversity, adaptability, and potential resilience against infectious diseases is essential to enhance conservation efforts for threatened species. Here, we describe the development of a custom 50K SNP array for Pseudophryne corroboree, a critically endangered amphibian threatened by the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) and illustrate its application in characterising the species’ genomic architecture. The array comprises 48,386 SNPs, with an average density of 5.45 SNPs per Mb and was effective in genotyping multiple tissue types, including non-lethal buccal swabs. Of the SNPs, 82.1% were polymorphic across 910 captive-bred P. corroboree individuals derived from 54 families. Our analysis of this population revealed evidence of ancestral inbreeding, the presence of two historic bottlenecks occurring approximately 100 and 10 generations ago, with the latter coinciding with the arrival of Bd to Australia. We also demonstrate the array’s cross-species amplification potential, successfully converting 21,077 (43.6%) polymorphic loci across three closely related anurans. This array is a valuable resource for future investigations aimed at understanding the genetic basis of disease resistance and developing management strategies for improving reintroduction outcomes in P. corroboree.