Historically, giraffe have been translocated across Africa to supplement extant populations, reintroduce extinct populations or to establish new populations, often for conservation and tourism. Such faunal relocations were often carried out disregarding taxonomic affiliation. Today, the small giraffe populations in the Republic of Malawi are assumed to consist of South African giraffe (Giraffa giraffa giraffa), which have likely descended from five individuals translocated from Imire Game Park (Zimbabwe) to Nyala Game Park (Malawi) in 1993. However, during the last 25 years, unknown additional translocations, migrations or unrecognized local populations of potential Masai giraffe (Giraffa tippelskirchi) in Malawi may have resulted in introgressive hybridization. Thus, the current taxonomic affiliation for Malawi’s giraffe is uncertain, calling for a genetic assessment to implement further management. We analyzed mitochondrial sequences and nuclear introns for 14 individuals, representing approximately half of the known Malawian population, to genetically determine the (sub)species of giraffe that occur in the Republic of Malawi by comparison with a comprehensive Giraffa dataset. Additionally, we genotyped individuals at ten microsatellite loci to determine the level of inbreeding and potential introgression. All data identify individuals unambiguously as South African giraffe, although two individuals shared a single nuclear allele with Masai giraffe. The low microsatellite genetic variability suggests high inbreeding in the current population. Thus, supplementing Malawi’s giraffe populations with G. g. giraffa will prevent further loss of their genetic diversity and avoid inbreeding depression.