The application of whole genome sequencing (WGS) for precise individual identification and kinship verification in veterinary forensics is not yet fully established. To evaluate the forensic utility of genomic profiling, we analyzed WGS data from post-mortem feline tissues suspected of animal abuse, alongside domestic cat reference genomes, identifying over 4.7 million high-quality single nucleotide polymorphisms (SNPs) from approximately 34 million raw variants. First, we established clear genomic evidence for individual identity and familial relatedness among the fragmented tissues. Through comparative population genomic analysis incorporating diverse pre-existing cat breeds, we evaluated the genetic structure and lineage of the specimens. Furthermore, targeted genetic screening provided molecular evidence for specific morphological traits, such as coat color phenotypes, which reflects the physical characteristics of the unidentified animal remains. Collectively, these findings highlight the efficacy of WGS as a robust and comprehensive analytical tool in veterinary forensics, offering critical evidence for resolving complex animal cruelty cases.