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NorA is one of the main native MDR efflux pumps of <i>Staphylococcus aureus</i>, contributing to reduced susceptibility towards fluoroquinolones and biocides, but little is known about its variability within <i>S. aureus</i> or its distribution and conservation among other staphylococci. We screened for sequences homologous to <i>S. aureus norA</i> and found it in 61 out of the 63 <i>Staphylococcus</i> species described. To the best of our knowledge, this is the first study to report the occurrence of <i>norA</i> across the <i>Staphylococcus</i> genus. The <i>norA</i> phylogenetic tree follows the evolutionary relations of staphylococci and the closely related <i>Mammalliicoccus</i> genus. Comparative analyses suggest a conservation of the NorA function in staphylococci. We also analyzed the variability of <i>norA</i> within <i>S. aureus</i>, for which there are several circulating <i>norA</i> alleles, differing up to 10% at the nucleotide level, which may hamper proper <i>norA</i> detection. We demonstrate the applicability of a PCR-based algorithm to detect and differentiate <i>norA</i> alleles in 52 <i>S. aureus</i> representing a wider collection of 89 isolates from different hosts. Our results highlight the prevalence of <i>norAI</i> and <i>norAII</i> in different settings and the association of <i>norA</i> alleles with specific <i>S. aureus</i> clonal lineages. Ultimately, it confirms the applicability of our PCR-based algorithm to rapidly detect and assign the different <i>norA</i> alleles, a trait that may impact antimicrobial efflux capacity and the search for potential NorA inhibitors.