<p>Sex determination systems in teleost fishes are highly diverse, and even closely related species often evolve different mechanisms. Although hybridisation among Eurasian minnows (<i>Phoxinus</i>: Cypriniformes, Leuciscidae) is well documented, their sex determination systems remain unexplored. Here, we investigated the genetic basis of sex determination in <i>Phoxinus phoxinus</i> and <i>Phoxinus csikii</i> using whole-genome sequencing, with a combination of coverage, SNP-, and k-mer-based approaches to identify sex-associated genomic regions. Whole-genome coverage analyses revealed no chromosomes with significantly sex-biased coverage, consistent with homomorphic sex chromosomes in both species. In <i>P. phoxinus</i>, male-specific heterozygosity at sex-linked SNPs showed genotypic differences within two regions, namely on chromosomes 3 and 12. Analysis of SNPs in these regions revealed drainage-specific, sex-associated patterns, indicating the presence of population-specific sex-associated genomic loci and a male heterogametic (XX/XY) system in this species. In contrast, <i>P. csikii</i> females displayed unique genotypic differences in a different part of chromosome 3, pointing to a female heterogametic (ZZ/ZW) system. We further observed overrepresentation of male-specific DNA sequences in <i>P. phoxinus</i> and female-specific sequences in <i>P. csikii</i>, providing additional evidence for the presence of sex-specific genomic regions and differing sex determination mechanisms in both species. These results provide evidence that two closely related <i>Phoxinus</i> species possess distinct sex determination systems, which may contribute to reproductive isolation.</p>