Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), occurs in all major wheat-growing regions worldwide and poses a constant threat to production. In South Africa, Pst first emerged in 1996 in the Western Cape and has since caused frequent epidemics with three further distinct races (pathotypes) recorded to date. Herein, we undertook detailed genomic-based analyses of four Pst isolates that represent the four dominant Pst races in South Africa recorded between 1996 and 2005. This analysis identified a number of polymorphic genes with features of known effector proteins and provided additional support of the likely stepwise changes in virulence profile of these South African Pst isolates. Next, we carried out comparative genomic-based analyses with 54 additional Pst isolates collected across wheat-growing regions within South Africa between 1996 and 2017 and 58 Pst isolates from East Africa, Pakistan, the UK, and France. This revealed a close genetic relationship between Pst isolates in South Africa and a number from East Africa. Furthermore, we found the South African Pst isolates also grouped closely with isolates identified in the UK in 2013 that were specifically found on triticale, illustrating long-distance transmission of Pst isolates either between these regions or from a common independent source area. This highlights the critical need for close monitoring of Pst. With wheat being the most planted winter cereal crop in South Africa, investment in continuous surveillance is essential to rapidly identify any future introductions that could quickly lead to rust epidemics.