Nucleotide diversity was examined at mitochondrial COI and r16S2 loci in eight Glossina swynnertoni Austen collections from northern Tanzania and from a culture maintained by the International Atomic Energy Agency. Eighteen composite haplotypes were observed among 149 flies, two of which were common to all samples and 10 were private. Mean haplotype diversity was 0.59 and nucleotide diversity was 0.0013. There were excess singular haplotypes and mutation-drift disequilibrium suggesting that populations had experienced an earlier bottleneck and subsequent expansion. Factorial correspondence analysis showed that haplotype frequencies varied much more temporally (GST = 0.18) than spatially (GST = 0.04). The estimate of effective population size Ne in Tarangire was a harmonic mean ~50 reproductive flies averaged over ~47 generations. The mean rate of gene flow was estimated to be ~5±1 reproducing females per generation but inflated because of mutation-drift disequilibrium arising from likely earlier bottlenecks.