Insertion sequences (IS) are small, transposable elements, commonly found in bacterial genomes. They are amongst the most dynamic components of bacterial genomes and can drive evolution through functional changes (interrupting or up-regulating genes); mediating gene deletion; or creating structural variation. The Shigella sonnei reference genome 53G contains over 200 different IS insertions. Whole genome phylogenetic analysis shows that there are three common lineages of S. sonnei. Variation caused by IS is often ignored in such analyses as these regions are difficult to extract from short read data. We developed a tool, ISMapper, to detect IS from short read data and used it to screen a global collection of S. sonnei isolates for the presence of 12 different IS. We found that each lineage has a unique IS profile and distinct IS dynamics. We used ancestral state reconstruction to infer the timing of IS gain and loss events on the tree. We estimate that the common ancestor of S. sonnei (circa 1669) carried 129 IS insertions, and that lineages 2 and 3 each accumulated ~120 additional IS by the mid 19th century and are now saturated at ~300 IS per genome. Lineage 1 accumulated only ~20 additional IS by the mid 19th century, but is now undergoing IS expansion, with current isolates still accumulating IS at a rate of ~0.3 copies/genome/year. Additionally, we detected hotspots for IS insertions, and showed that IS are major contributors to gene inactivation which has played a significant role in S. sonnei evolution.