Clonality plays an important role in the proliferation of invasive species and, when coupled with loss of seed viability, can facilitate invasive success by reducing reliance on sexual reproduction and promoting spread of genetically identical individuals. Clonal invasions are advantageous for biological control strategies, as biological control agents may have a uniformed, damaging response to invasive populations with low genetic diversity. Agents sourced in the native range that are locally adapted to the same plant genotype that is invasive, may cause this response. Understanding the population genetics and invasion history of a species in the novel range is paramount to ensure effective biological control agents are introduced. Here we investigated the population genetics of pickerelweed (Pontederia cordata L.), a tristylous invasive macrophyte native to North and South America causing detrimental impacts in South Africa (SA). SA populations all have only one of three tristylous forms and produce no seeds. Inter Simple Sequence Repeats (ISSR) of P. cordata leaf samples from SA and from parts of the native range in the United States of America (USA) were used to determine population structure and potential source populations. Pontederia cordata has low genetic diversity within and amongst invasive populations in SA compared to native populations. This suggests no sexual reproduction and limited gene flow in SA, and only one introductory event. Invasive populations shared the closest genetic similarity with native samples from Virginia, USA, and although large parts of the indigenous distribution were not sampled, this close match suggests that the site may be a suitable area to source potential biological control agents. However, genetic sampling in other native areas should also be considered to confidently determine the origin of SA populations. This study corroborates other global findings of highly successful invasive species utilizing clonality, and consequently, resulting in invasive genotypes with low diversity.