The Cuvier's beaked whale, Ziphius cavirostris, is a cosmopolitan species and the only beaked whale species commonly found in the Mediterranean Sea. Five strandings of Cuvier's beaked whale were reported along the Aegean/Mediterranean Seas coasts of Türkiye and northern coast of Cyprus in 2016–2017. Mitochondrial DNA (mtDNA) control region (430–444 bp) and cytochrome b (cytb) (382–424 bp) sequences each revealed two different haplotypes (four out of five individuals had the same haplotype for each locus) on these stranded animals. The control region haplotypes were identical to two previously identified haplotypes from the Ionian (Greece) and Adriatic (Croatia) Seas. Only one of the cytb haplotypes had previously been described from the Adriatic Sea (Italy) and the other one was detected for the first time. In a comparison of these haplotypes with Cuvier's beaked whale haplotypes previously reported from outside the Mediterranean Sea, the Mediterranean subpopulation shows genetic differentiation based upon the presence of two unique haplotypes. Additional mtDNA sequences from the Mediterranean Sea are needed for a better understanding of the genetic population structure of this species and to elaborate more concrete conservation measures.