The genus Solenopsis appears to have evolved and radiated very rapidly in South America and then spread throughout the rest of the continent. As part of the expansion process, distribution patterns and different degrees of geographic isolation among populations of S. saevissima can be observed. We have investigated the presence of Wolbachia in 52 colonies and 1623 individuals in southeastern Brazil. Detection of Wolbachia infection was based on amplification of the 16S rRNA and wsp genes by polymerase chain reactions. Wolbachia was found in only one of the four locations investigated and it was observed that the populations were polymorphic for infection. The infection level observed increased during the period of screening. In particular, double infection (16SWA and B) increased from 44% in 2005 to 90% in 2006. The A-group of Wolbachia from the wsp sequences was determined by sequencing. However, two variant wsp sequences were detected in Wolbachia present in these populations. The alignment of our sequences with those deposited in GenBank indicated significant differences in relation to homologous sequences. Phylogenetic relationships were inferred using parsimony, and confidence intervals were estimated by bootstrapping. Then the divergence of the Wolbachia of S. saevissima in the populations studied with other variants allowed us to verify that wSS1 and dwSS2 formed a distinct clade within the A-group (> 75%). These results can be useful in studies on the dynamics of ant populations.