Hybridization between milky stork (Mycteria cinerea) and painted stork (M. leucocephala) occurs frequently in captivity. Dusit Zoo is a captive breeding facility where storks with phenotypically ambiguous patterns have recently been observed, and their status remaining inconclusive. Here, we used a combination of phenotypic characters and genetic markers (cytochromeband 14 microsatellite markers) to distinguish and identify hybrids from the two parental species (n= 114). Haplotype analysis revealed asymmetric mtDNA introgression fromM. cinereatoM. leucocephala, with twelve morphologically classifiedM. leucocephalaindividuals carrying heterospecific mtDNA. Comprehensive biparental genetic assessments identified 33% of all three genetic clusters as admixed individuals, of which most were either F2 hybrids, backcrosses withM. leucocephala, or hybrids of unknown generation, implying weak premating isolation with the absence of intrinsic postzygotic isolation between parentals. Morphological analysis demonstrated that the absence or indistinctness of a black bar across the breast is the most noticeable trait to identify these hybrids. The endangeredM. cinereawas found to have genomic contamination fromM. leucocephalaand vice versa, with at least 41 hybrid individuals being identified. These findings provide critical information for detecting hybrids and identifying suitable breeding stocks with genetic purity for future reintroduction and conservation management.