Croatian cattle breeds are deeply rooted in the agricultural history of Croatia. Today, they are not involved in production due to the introduction of imported commercial breeds. However, Croatian cattle breeds possess resistance genes that are the result of local adaptations, which justifies the need for their conservation. These breeds have developed and adapted to various geographical regions of the Republic of Croatia, reflecting those conditions in their appearance and adaptability. In this research, the Illumina Bovine HD BeadChip (777 K) was used, and a total of 674 cattle were divided into 25 breeds. The key information contained in these SNPs was used in further analyses of genetic diversity and population structure. The aim of the study was to identify the genetic introgression within Croatian cattle breeds. The Slavonian-Syrmian Podolian was identified as a separate breed early in the analysis. Buša and the Istrian cattle frequently grouped together in principal component analyses and neighbor-net networks. Population structure analyses indicate high levels of admixture within the Buša breed, while somewhat lower levels were observed within the Istrian cattle. The Slavonian-Syrmian Podolian again stood out as distinct from all other breeds in the structure analyses. Analyzes of gene migration did not show gene flows between Croatian and local breeds, like Italian and commercial breeds. The results of this study highlight the genetic distinctiveness of Croatian cattle breeds compared to other breeds, confirming their unquestionable status. For more precise and reliable analysis, it is necessary to increase the sample size and include additional methods for identifying introgression.