Abstract
Effective management decisions rely on accurate insights into species’ population structure, with high-quality genetic material being essential. Stranded cetaceans are an important source of samples, but meeting quality standards remains challenging. Despite their frequent use in conservation genetics, no controlled studies have compared DNA yield and quality across tissue types and preservation methods. This is further compounded by cetaceans uniquely derived physiology, meaning standards obtained from other mammals might not apply. In this study, we compared DNA concentration, purity, and integrity when extracted from skin, muscle, and blubber samples preserved in 96% ethanol or frozen at − 20 °C. Samples were obtained from a tissue bank of stranded dolphins and classified into five decomposition condition categories following international guidelines. All samples underwent standardized protocols for DNA extraction, quantification, and quality control. Statistical analyses evaluated the influence of tissue type and preservation method on DNA quality. Skin consistently produced the highest DNA concentrations and acceptable purity levels, even in advanced decomposition stages. DNA integrity declined with decomposition, except in muscle, which retained higher integrity values in later stages. Both 96% ethanol and freezing at − 20 °C produced good results in early decomposition stages, while freezing was particularly important for maintaining DNA integrity in muscle in more advanced decomposition. Based on these findings, we propose two frameworks: one guiding researchers according to sequencing requirements, and another simplified version for stranding networks. These results contribute to standardized sampling protocols and improve the reliability and comparability of genetic analyses from stranded cetaceans. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41686-x.