Cryptic species are likely an important source of undescribed diversity, of which algae are prime examples with convergent morphologies and complex life cycles. Novel methods are needed to better characterize their diversity, one avenue being the exploration of their relationships with other organisms, such as the herbivores that feed upon them. However, even when assessing generalist diets, it is unclear how representative this diversity is of the algal community at large. In this study, we applied a metabarcoding approach to marine, epilithic algal communities across the Main Hawaiian Islands (MHI) to catalog siphonous algal diversity. This approach recovered 92 OTUs of siphonous green algae, 39 of which are statistically supported as putative undescribed species. Comparison of this community inventory with that recovered from the “stolen chloroplasts”, or kleptoplasts, of the sea slug Plakobranchus cf. ianthobapsus, which is known to target cryptic and diminutive siphonous green algae as kleptoplast sources, revealed that P. cf. ianthobapsus only utilizes 25% of the available diversity and that there is high phylogenetic affinity of kleptoplast diversity: the sacoglossan almost exclusively sequesters chloroplasts from species in the suborder Halimedineae. The community inventory of siphonous algal diversity detected well-established and new populations of the highly invasive alga Avrainvillea lacerata on the islands of O‘ahu and Maui, respectively, but was unable to confirm previous records from Kaua‘i. Comparison of diversity data generated from multiple sources, in this case epilithic algal communities and algivore associations, provides a multifaceted view into these relationships, algal diversity, and their ecology.