Apoptosis or programmed cell death is the result of complex biochemical and genetic signals triggered by normal physiological events or by exposure to toxic compounds. Apoptosis can be revealed early in cells and tissues due to morphological and biochemical alterations of the cell. Here, we review recent progress in the study of the induction and detection of apoptosis in zooplankton copepods after their exposure to different apoptotic-inducer compounds, and we propose methods to predict copepod mortality even when animals appear normal. We also discuss the use of higher harmonic generation microscopy and multiphoton fluorescence microscopy techniques as possible tools to visualize apoptosis in vivo copepods without using any fluorescent probes.