Corals are threatened worldwide due to rapidly warming oceans associated with anthropogenic climate change. Increasing temperatures can lead to coral bleaching, which is the loss of the obligatory symbiotic relationship between the coral host and their algal symbionts. However, some corals are facultatively symbiotic and can thrive both with and without symbionts. Facultative corals, therefore, offer an interesting model system for understanding the mechanisms governing coral bleaching, which is critical knowledge for protecting these ecosystem engineers under a changing world. Quantifying levels of symbiosis remains a challenge, and existing methods require the destruction of the coral in order to determine symbiont densities. Here, we develop a non-invasive image-based analysis of pigment density for two facultatively symbiotic corals, which naturally exist both as symbiotic and aposymbiotic colonies, which will help further develop these species as models for coral bleaching. Images of corals that varied in their symbiont densities were analyzed with ImageJ and algal densities were approximated via modified MATLAB scripts. Estimated algal densities were correlated with relative proportions of algal symbiont reads to total coral plus symbiont (holobiont) reads via tag-based RNA sequencing. Our photographic assessments of Oculina arbuscula, but not Astrangia poculata, correlated well with symbiont densities from RNAseq data, which suggests that although these image-based analyses can provide an accurate, rapid, and scalable assessment of algal symbiont densities, they must be further developed to specific species.