AbstractMarine heatwaves (MHWs) are a growing threat to marine species globally, including economically and ecologically important foundation species, such as seagrasses. Seagrasses in tropical regions may already be near their thermal maxima, and, therefore, particularly susceptible to increases in temperature, such as from MHWs. Here, we conducted a 10‐day MHW experiment (control +4°C) to determine the effects of such events on the two tropical seagrasses Halophila beccarii and Halophila ovalis. We found that both species were largely resistant to the MHW, however, there were differences between the species' responses. For H. beccarii, the surface area of existing leaves was smaller under MHW conditions, yet a substantial increase in the number of new leaves under the MHW indicated its tolerance to—or even increased performance under—the MHW. While there was no direct effect of the MHW on H. ovalis, this species saw less epiphyte biomass and percentage cover on its leaves under the MHW. While a lower epiphyte cover can potentially increase the health and ecophysiological performance of the seagrass, the change of epiphytes can lead to bottom‐up trophic implications via the influence on mesograzer feeding. Together, the results of this study demonstrate the species‐specific responses of seagrasses of the same genus to a warming event. With the current global decline of seagrasses, our results are encouraging for these important habitat formers as we show that anomalous warming events may not necessarily lead to ecosystem collapse.