Computer assisted movement tracking was used to characterize the motility of two marine microalgae, Isochrysis galbana and Tetraselmis chui, and to investigate the toxicity of Cu, Pb, and Cd on motile percentage, curvilinear velocity, average path velocity, straight line velocity, linearity, straightness, and wobble. Except for motile percentage, all other motility parameters differed significantly between I. galbana and T. chui. Based on relative motile percentage data, the median effective concentration (EC50) of Cu on the motility of I. galbana and T. chui was 31.4 and 1.3 μmol/L, respectively, while for Pb it was 37.8 and 10.9 μmol/L and for Cd it was 121.6 and 37.8 μmol/L, respectively. Compared to I. galbana, T. chui was more sensitive to all tested metals. The toxic effect of the heavy metals on motility exhibited the following decreasing order for both species: Cu > Pb > Cd. Our results indicate that I. galbana and T. chui motility is sensitive to heavy metals and can be used as an indicator for toxicology bioassays.