The invasive fruit-pest Drosophila suzukii is characterized by a specific fresh-fruit targeting behavior and has quickly become a menace for the fruit economy of newly infested North American and European regions. D. suzukii carries a strain of the endosymbiotic bacterium Wolbachia, named wSuz, which has a low infection frequency and no reproductive manipulation capabilities in American populations of D. suzukii. To further understand the nature of wSuz biology and assess its utility as a tool for controlling this pest populations, we investigated the prevalence of Wolbachia in 23 European D. suzukii populations, and compared our results with those available in American populations. Our data showed a highly variable infection frequency with a mean prevalence of 46%, which is significantly higher than the 17% found in American populations. Based on Multi-Locus Sequence Typing analysis, a single wSuz strain was diagnosed in all European populations of D. suzukii. In agreement with American data, we found no evidence that wSuz induced significant cytoplasmic incompatibility. These findings raise not only the question of maintenance of Wolbachia in field populations of D. suzukii but also of the selective forces responsible for a) the overall higher Wolbachia prevalence in European than in American populations of D. suzukii and b) the variation in prevalence within populations. Our results provide new insights into the D. suzukii-Wolbachia association and highlight regional variations. These variations await further investigation to determine their causes and should be taken into account for using Wolbachia-based pest management programs.