Whole genome sequencing has enhanced surveillance and facilitated detailed monitoring of transmission of Shigella species in England. We undertook an epidemiological and phylogenetic analysis of isolates from all cases of shigellosis referred to Public Health England between 2015 to 2018 to explore recent strain characteristics and transmission dynamics of Shigella species. Of the 4950 confirmed cases of shigellosis identified during this period, the highest proportion of isolates were S. sonnei (54.4%), followed by S. flexneri (39.2%), S. boydii (4.1%) and S. dysenteriae (2.2%). Most cases were adults (82.9%) and male (59.5%), and 34.9% cases reported recent travel outside the UK. Throughout the study period diagnoses of S. flexneri and S. sonnei were most common in men with no history of recent travel abroad. Species prevalence was not static with cases of S. flexneri in men decreasing between 2015-2016, and the number of cases of S. sonnei increasing from 2017. Phylogenetic analysis showed this recent increase in S. sonnei was attributed to a novel clade that emerged from a Central Asia sub-lineage, exhibiting resistance to ciprofloxacin and azithromycin. Despite changes in species prevalence, Shigella diagnoses in England are persistently most common in adult males without reported travel history, consistent with sexual transmission amongst men who have sex with men. The trend in increasing ciprofloxacin resistance in S. sonnei, in addition to plasmid-mediated azithromycin resistance, is of significant public health concern with respect to transmission of multi-drug resistant gastrointestinal pathogens and the risk of treatment failures.