Ostreopsis siamensis is a morphologically cryptic marine protist (Alveolata: Dinophyceae) that produces toxic and complex non-peptide compounds, palytoxins (PLTX). The intraspecific genetic diversity of marine protists across environmental gradients of tens to hundreds of kilometres is still relatively little known, and the extent to which these differences are linked to functional traits has largely not been explored. Despite a widespread distribution along the East Australian coastline, and ecologically detrimental blooms of O. siamensis, little is known about the interspecific genetic and phenotypic diversity driving PLTX biosynthesis amongst their populations. Such information is important in furthering our understanding of likely changes in the populations of this species, as the East Australian Current is considered a ‘climate change hotspot’, with increases of up to 2.0 °C over the past 100 years, and a more southern range extension. In our study, we analysed ribosomal (rDNA) data, morphological features, photophysiological traits (FRRf) and toxin profiles (LC-MS/MS) from 55 O. siamensis clonal isolates from 8 different sites along the east Australian coastline, to determine the cooperative and specific traits amongst and between different geographic populations that promote the ecological success of this species. RNA sequencing (RNA-seq) analyses were performed to identify genes encoding for key metabolic pathways such as toxin biosynthesis. Our findings suggest that O. siamensis may allow mutualistic intraspecific facilitation in multiple ways, thereby promoting the overall success of the species and facilitation of its expansion.