IntroductionStranding networks are invaluable sources of biological data and material for marine mammals. Such data helps gaining a comprehensive knowledge of their population dynamics, which is an essential requirement for several downstream applications including management decisions for effective marine mammals conservation. However, gathering such information is particularly challenging due to their highly mobile and often elusive nature1. In this regard, genetic analysis provides a powerful tool for studying cetacean ecology, evolution, and conservation. Genetic data facilitate the assessment of population structure, connectivity, and gene flow, which are crucial for identifying distinct populations and their migration patterns2,3. Moreover, genetic studies contribute to understanding the evolutionary relationships among species, aiding in reconstructing their phylogenetic history4. From a conservation perspective, genetic markers help delineate management units and identify demographic groups that may be more vulnerable to environmental changes or anthropogenic threats5. The use of genetic techniques also extends to health assessments, where molecular methods can evaluate the genetic basis of disease resistance or susceptibility in cetacean populations6. Such insights inform targeted conservation strategies, ensuring the long-term viability of these species in the face of anthropogenic pressures, habitat degradation, and climate change1.Despite the value of genetic research in cetacean conservation, acquiring high-quality samples from live animals presents logistical, financial, and ethical challenges7,8,9. Sampling of internal tissues requires highly invasive techniques that are not ethically feasible for marine mammals. Minimally invasive techniques such as skin and blubber biopsies still require specialized equipment, trained personnel, and consideration of potential stress inflicted on the animals8. Dead stranded cetaceans, on the other hand, are not subject to such limitations and offer a unique research opportunity by providing access to a wide range of tissue types, including internal organs and blood, which are often unavailable in live sampling9. Accordingly, over the last decades, cetacean researchers have relied on stranding material to obtain DNA for a range of genetic studies3,10,11. However, a significant limitation is the degradation of genetic material due to decomposition, which can hinder the accuracy of analyses12,13,14. Environmental factors, such as temperature, salinity, contamination, and scavenger activity, further complicate sample preservation15. Therefore, researchers working on DNA from stranded samples commonly experience considerable variation in success rate between samples, involving unavoidable waste of time and lab resources processing samples whose DNA is not usable for many downstream analyses.To mitigate these challenges, standardized protocols for tissue collection and preservation from stranded cetaceans must be refined to optimize resulting DNA integrity and help ensuring reliable results are obtained ahead of any experimental work. While stranding networks generally adhere to standardized guidelines established by national programs or international reference societies9,16,17, they do not all follow unique tissue sampling protocols for downstream DNA analyses. Such standardization is necessary to ensure sample quality consistency, as it enables uniform data collection which is vital for comparing and integrating data from different regions and networks18,19. Sampling frameworks should cover both methodological approaches to tissue collection and preservation strategies based on the animal’s decomposition. Furthermore, sampling and storage guidelines should offer options tailored to tissue banks facing economic and logistical (e.g. field conditions) challenges.While dedicated sampling guidelines for genetic analysis have been developed19,20, including a thorough sampling framework covering sample type, storage, and genetic applications, they are not informed by a systematic comparative analysis of the efficiency of different preservation methods and tissue matrices regarding DNA quality parameters. Such comparisons have been conducted for other taxonomic groups21, but cetacean physiology is uniquely derived compared to terrestrial mammals, and therefore a dedicated study is required but is currently lacking. In this study, we assessed the influence of different tissue matrices (skin, blubber, and muscle) and preservation methods (96% ethanol and freezing at − 20 °C) on DNA quality parameters such as DNA concentration (ng/mL), purity (absorbance ratios 260/280 and 260/230), and integrity (DNA integrity number, DIN, a numerical assessment of DNA fragmentation) across different decomposition condition categories (DCC) in stranded small cetaceans. Additionally, we examined the interplay of these variables with storage time, and their impact on final DNA quality outcomes. This study aims to advance knowledge on sampling and preservation protocols that can be applied to stranding networks worldwide, particularly those with limited financial resources, to facilitate the collection of high-quality samples for genetic analysis in small cetaceans.ResultsInfluence of tissue matrix, decomposition condition category (DCC), preservation method and storage time on DNA quality measuresThe influence of the analyzed variables on DNA concentration (ng/µL) differed between both measuring instruments (i.e. NanoDrop 1000 Spectrophotometer and Agilent TapeStation system).Measurements using the NanoDrop (ND) revealed that the tissue matrix (p