The cells and tissues of many marine invertebrates and their associated flora contain fluorescent pigments and proteins, many of which have been utilized commercially and provide marker molecules in other systems for fluorescence imaging technology. However, in the study of marine invertebrates and their symbioses these naturally occurring molecules have been seen to limit or confound fluorescence microscopy analyses. Here we demonstrate the endogenous fluorescence associated with two marine invertebrates (coral and foraminifera) and describe how these qualities can be utilized in fluorescence microanalyses. Understanding and imaging the diversity of fluorescent molecules provide insight into how fluorescence microscopy techniques can now be applied to these complex systems.