Microscopy techniques have been widely applied to observe cellular ultrastructure. Most of these techniques, such as transmission electron microscopy, produce high-resolution images, but they may require extensive preparation, hampering their application for in vivo examination. Other approaches, such as fluorescent and fluorogenic probes, can be applied not only to fixed specimens but also to living cells when the probes are nontoxic. Fluorescence-based methods, which are generally relatively easy to use, allow visual and (semi)quantitative studies of the ultrastructural organization and processes of the cell under natural as well as manipulated conditions. To date, there are relatively few published studies on the nearly ubiquitous marine protistan group Foraminifera that have used fluorescent and fluorogenic probes, despite their huge potential. The aim of the present contribution is to document the feasible application of a wide array of these probes to foraminiferal biology. More specifically, we applied fluorescence-based probes to study esterase activity, cell viability, calcium signaling, pH variation, reactive oxygen species, neutral and polar lipids, lipid droplets, cytoskeleton structures, Golgi complex, acidic vesicles, nuclei, and mitochondria in selected foraminiferal species.