A gram-negative bacterium was isolated from a cerebrospinal fluid sample from an HIV-seropositive Rwandan refugee with primary meningoencephalitis. This Marseille-Goma sample B isolate, strain MGBT (T = type strain), was found to exhibit evolutionary homology with Stenotrophomonas maltophilia, as determined by a 16S rRNA gene sequence analysis, and this finding was reflected by similar phenotypic traits. MGBT could, however, be distinguished from the S. maltophilia type strain by using a number of biochemical and physiological tests, and a genotypic analysis of the two strains in which DNA homology was used revealed only 35% homology between them. Furthermore, the antibiotic susceptibility of MGBT was restricted to netilmicin, ciprofloxacin, trimethoprim-sulfamethoxazole, and colimycin. On the basis of these results we propose that MGBT is a representative of a new species in the genus Stenotrophomonas, Stenotrophomonas africana.