<p><i>Rhipicephalus sanguineus</i> is a tick species characterized by high intraspecific variability, even among populations occupying the same habitats. This study investigated whether two distinct phenotypes of <i>R. sanguineus</i>, collected from four geographically separated regions, are associated with specific nucleotide polymorphisms in the mitochondrial <i>cox</i>1 and 16S rRNA gene regions—markers commonly employed in phylogenetic analyses. Morphometric analysis based on established criteria clearly distinguished two morphotypes—Morphotype 1 and Morphotype 2—with statistically significant differences. This morphological differentiation was supported by phylogenetic and genetic divergence analyses, primarily based on mitochondrial <i>cox</i>1 sequences, which revealed six polymorphic sites within the analyzed fragment. Among the identified haplotypes, two—Haplotype 2a and Haplotype 2b—were consistently associated with Morphotype 2. This genetic segregation was confirmed in extended analyses including reference isolates (morphologically and/or genetically defined either as <i>R. sanguineus</i> or <i>R. hibericus</i>). These analyses also demonstrated a close phylogenetic relationship between Morphotype 1 and the <i>R. sanguineus</i> neotype, as well as between <i>R. hibericus</i> and both morphotypes. Although the 16S rRNA marker exhibited lower resolution, it still effectively distinguished the two morphotypes and corroborated the haplotype assignments established by the <i>cox</i>1 phylogeny. The observed genetic divergence (p-distance of 1% in <i>cox</i>1 gene) and the phylogenetic relationship between <i>R. sanguineus</i> and <i>R. hibericus</i> confirmed that <i>R. sanguineus</i> is a polymorphic species, with well-defined haplo-morphotypes, and that <i>R. hibericus</i> is not genetically distinguishable from <i>R. sanguineus</i>.</p>