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We investigated the prevalence and genetic diversity of <i>Wolbachia pipientis</i> strains in <i>Aedes albopictus</i> populations in Greece. Using a combination of PCR and Sanger sequencing techniques, we genotyped <i>Wolbachia</i> strains in 105 mosquitoes collected across eight different administrative regions in 2021. We found a high prevalence of <i>Wolbachia</i> in both male (90%) and female (97%) mosquitoes. Among the infected samples, 84% had double infections with both <i>w</i>AlbA and <i>w</i>AlbB strains, while 16% had infections with only <i>w</i>AlbB. Our comparison of the Multi-Locus Sequence Typing (MLST) profile, employing <i>gatB–coxA–hcpA–ftsZ–fbpA</i> genotyping, revealed a single MLST profile for each <i>w</i>AlbA and <i>w</i>AlbB strain in Greek populations. The same MLST profiles were also reported in populations from China, Russia, and Argentina, suggesting low levels of global diversity in <i>w</i>AlbA and <i>w</i>AlbB strains. Furthermore, our results indicated a significant association between temperature and the prevalence of single infections (<i>p</i> = 6.498 × 10⁻⁷), with higher temperatures correlating with an increased likelihood of single infections. Although male bias showed a tendency towards single infections, the effect was marginally non-significant (<i>p</i> = 0.053). These results were confirmed using a bootstrap-with-replacement analysis approach. Overall, our findings offer novel insights into the distribution and species diversity of <i>Wolbachia</i> strains in Greek <i>Ae. albopictus</i> populations, emphasizing the importance of understanding the short-term plastic and adaptive responses of these organisms to environmental stressors and rapid climate change.