Over the last century, invasive species have emerged as an important driver of global biodiversity loss. \textitLantana camara is one of the hundred most problematic invasive species globally, yet its genetic diversity patterns remain poorly understood. Previous studies hypothesize that invasive \textitL. camara is a species complex of hybrid origin, though this remains untested. We investigated the population genetic patterns of \textitL. camara by sampling 359 plants representing diverse flower colour variants across 36 locations in India. Analyses of the population structure using 19,008 SNPs revealed a strong genetic structure in India. However, this structure showed little correlation with geography; instead, individuals with similar flower colours clustered together irrespective of location in the structure analysis. Low genetic distance between most of the individuals indicated the absence of multiple species. A high inbreeding coefficient and low proportion of heterozygous sites suggested predominant self-fertilization, confirmed by bagging experiments. Thus, we infer that \textitL. camara exists as homozygous inbred lines formed by self-fertilization, associated with distinct flower colours. These results refute the hypothesis that \textitL. camara is a species complex. Our findings highlight a hitherto unknown role for mating systems in invasive species, furthering our understanding of evolution in invasive species.