<p class="IsiAbstrakIndo"><span lang="EN-GB">Phylogenetic or population genetic studies have been focused on finding genetic variations in mitochondrial DNA (mtDNA) because mutations in this region contained five times higher than other genetic materials. The aim of this research was to generate PCR-RFLP D-loop mtDNA profiles of some Indonesian domestic waterfowl. The samples were 35 local ducks, 5 muscovy duck, and 5 geese. These local ducks included on seven types of Javanese ducks in Central Java, i.e. Magelang duck, Peking duck, Pengging duck, Tegal Branjangan duck, Tegal Jarakan duck, Tegal Blorong duck, and Tegal Lemahan duck. PCR technique was used to amplify the D-loop genes, and RFLP analysis of the D-loop was performed with </span><em><span lang="EN-GB">Alu</span></em><span lang="EN-GB">I</span><em></em><span lang="EN-GB">and </span><em><span lang="EN-GB">Rsa</span></em><span lang="EN-GB">I. The results show that muscovy duck has no restriction sites in D-loop gene. Moreover, goose has a restriction </span><em><span lang="EN-GB">s</span></em><span lang="EN-GB">ite of </span><em><span lang="EN-GB">Alu</span></em><span lang="EN-GB">I in D-loop gene at 550 bp and 187 bp; and it has no restriction site of </span><em><span lang="EN-GB">Rsa</span></em><span lang="EN-GB">I. The analysis of </span><em><span lang="EN-GB">Rsa</span></em><span lang="EN-GB">I-RFLP in mtDNA </span><em><span lang="EN-GB">D-loop </span></em><span lang="EN-GB">region of ducks resulted in 1 restriction fragment pattern which can be applied in the identification of duck to differentiate it from goose and muscovy duck. PCR-RFLP analysis duck D-loop mtDNA using </span><em><span lang="EN-GB">Alu</span></em><span lang="EN-GB">I and </span><em><span lang="EN-GB">Rsa</span></em><span lang="EN-GB">I restriction enzyme resulted in 3 combinations of restriction fragment pattern shown in 3 haplotypes (A, B, and C). Genetic diversity of Indonesian domestic waterfowl population could be identified by using PCR-RFLP analysis on mtDNA </span><em><span lang="EN-GB">D-loop </span></em><span lang="EN-GB">region. So far, there are few results of research on Indonesian domestic waterfowl genetic characteristics based on PCR-RFLP mtDNA D-loop marker. Also, this research has a good contribution on genetic characterization of local duck. The characterization is an important aspect to maintain breed quality and manage the genetic resources of Indonesian germplasm and in facilitating the breeding program. </span><strong></strong></p>