Most of the current knowledge about African tephritids originates from studies performed in agricultural areas, while information about their distribution in pristine or moderately disturbed environments is extremely scarce. This study aims at (i) describing levels of spatial variability of frugivorous tephritids in tropical forests and small rural villages of the Congo River basin and (ii) verifying if human-mediated activities, such as small-scale agriculture and trade, can affect their distribution patterns. Four locations were sampled along a 250 km stretch of the Congo River. At each location, pristine and disturbed habitats (i.e. tropical forests and small rural villages, respectively) were sampled, with three replicate sites in each combination of habitat and location. Sampling with modified McPhail traps baited with four different attractants yielded 819 tephritid specimens of 29 species from seven genera (Bactrocera, Carpophthoromyia, Ceratitis, Dacus, Celidodacus, Perilampsis, Trirhithrum). The three most abundant species sampled (Dacus bivittatus, D. punctatifrons, Bactrocera invadens) showed significant variations in abundance across locations and sites and accounted for 98.29% of the overall dissimilarity between habitats. Assemblages differed among locations and sites while they showed significant differences between pristine and disturbed habitats in two out of the four locations. This study shows that frugivorous tephritids in central Congo have remarkably patchy distributions with differences among locations and sites representing the main source of variability. Our data show that, in rural villages of central Democratic Republic of Congo, human activities, such as small-scale agriculture and local commerce, are not always sufficient to promote differences between the tephritid assemblages of villages and those of the surrounding tropical forests.