Proliferations of benthic harmful filamentous cyanobacteria belonging to the genus Microcoleus are expanding globally, but the effect of climate change on their success is not well known. We used four unialgal monoclonal non-axenic strains of Microcoleus, three of which produce both ATX and dhATX, in manipulative lab experiments to test their growth response to three different culturing temperatures (10, 20, and 30 °C). The toxic strains originate from streams in different climate zones and ecoregions- South Fork Eel River (Mediterranean California), a small tributary to Virgin River in Zion National Park (North American desert with cold semi-arid climate), and North Fork Shenandoah River (Eastern temperate forest with humid continental hot summers and year-round precipitation). We isolated a toxic and non-toxic strain from the same locality in Eel River. The strains were grown in 20 mL of BG11 medium under a light irradiance of 100 µmoles/m2/s on a 12:12 light:dark cycle in triplicate vials for chlorophyll a and cell density/biovolume measurements. The material was harvested along the growth cycle at days 7, 14, 21, 28, and 35. We used the Gompertz model to calculate the maximum growth rates based on pigment data. All strains grew best at 20 °C, achieving at least 1.23 times higher growth rates than other temperatures. Both strains from Eel River had higher growth rates at 10 °C compared to 30 °C, while the opposite trend was true for the strain from Shenandoah River. The strain from the Virgin River watershed had very little difference between the two temperatures. Microcoleus strains may represent different species, which will be identified based on genome analysis. This study showed that toxic Microcoleus species are adapted to their local climate conditions and respond differently to temperature extremes, which may be relevant to mitigating efforts in the changing climate.