As there was such a strong temporal signature for the number of observed mutations in the global S. sonnei population (Holt et al., 2013), we explored the temporal structure of the S. sonnei isolated in Bhutan using Bayesian phylogenetic methods. To do this, the nucleotide substitution rate of the primarily Bhutanese lineage of Central Asia was determined to be 7.34 × 10− 7 substitutions per site per year [95 % highest posterior density (HPD): 5.87 × 10− 7 to 8.83 × 10− 7], which is comparable to the previously calculated substitution rate of S. sonnei lineage III (Holt et al., 2013). Using these data, we estimate that the most recent common ancestor (MRCA) of the Bhutanese S. sonnei existed around 2006 (95 % HPD 2005–2007), with the majority diverging from a hypothetical MRCA around 2007 (95 % HPD 2005–2008) (Fig. 2). The results of this analysis were further supported by the linear relationship between root-to-tip branch length and date of isolation (R2 = 0.8412). Since its projected introduction in 2006, this S. sonnei lineage diverged into at least four sublineages (labelled A, B, C and D in Fig. 2), which have been transmitted endemically within the Bhutanese capital, Thimphu: isolates taken from cases in June/July 2011 (25/71 isolates) were found to belong to two subpopulations (A and C). Sublineage B, which was not represented in June/July 2011, dominated in the subsequent years (Fig. 2).