With the advancement of forensic genetics, an increasing number of non-human biological evidence samples have been recognized as crucial evidence in case investigations and judicial proceedings, primarily involving non-human individual identification, kinship analysis, and species identification. However, unlike non-human individual identification and kinship analysis, which can rely on STR genotyping systems, the technical approach for non-human species identification involves interdisciplinary fields such as evolutionary biology, and the uncertainty associated with its application in forensic practice has not yet been systematically quantified. In this study, species identification in shark was taken as an example to systematically investigate uncertainties arising from reference database curation, DNA barcode screening, and the determination of identification threshold values. For species identification involving bulk commodities, a simple random sampling approach was further established. Moreover, for species identification involving mixed samples, mixture ratio estimation was explored using high-throughput sequencing technology combined with a mitochondrial purification strategy. This study is expected to provide a scientific basis for standardizing species identification practices, particularly with respect to sampling strategies and mixture ratio estimation.