Varroa mite threatens honey bees worldwide by affecting larvae and adults and causing viral diseases associated with colony collapse. This study investigates its prevalence and infestation level, and morphometric traits in Southern Sudanese (SS) and Northern Sudanese (NS) phytogeographical zones of Burkina Faso. We visited 238 hives from 48 apiaries in 9 provinces. Phoretic varroa mites were detected through a 70% alcohol wash on approximately 300 worker bees. Once in the laboratory, 7 morphometric characters were measured on 1 to 10 varroa mites per hive. According to these measurements, the mites were identified as Varroa destructor, Anderson & Trueman, 2000. Data analysis reveals that 91.6% of colonies of the whole sample are infested with varroa. In NS zone, the provinces of Bazega and Zoundweogo show high infestation level (5.93% and 7.18% respectively), while in the SS zone, Nahouri and Ziro exhibit the highest level (8.19% and 9.00%) respectively. In terms of body length and body width (BL and BW), varroa mites from SS zone display averages of 1176.04 ± 40.1 µm and 1765.14 ± 49.2 µm, while those from the NS zone have average values of 1167.44 ± 40.8 µm and 1755.36 ± 53.42 µm. These morphological differences are statistically significant (P ≤ 0.05), highlighting variability that may result from local adaptations or genetic variations. The morphological diversity of this parasite has implications for its biology, dispersion, and virulence towards bees. Future studies should explore genetic factors influencing parasitic dynamics and bee resistance for effective management strategies.