The kleptoplastidic sea slug Plakobranchus cf. ianthobapsus is the only known herbivore of the invasive alga Avrainvillea lacerata in the Hawaiian Islands. Metabarcoding of the slug kleptoplasts detected new populations of the invasive alga, indicating broader surveys of algal algal communities from additional sites are needed to determine the extent of the A. lacerata invasion in Hawaii. Species discovery methods were applied to epilithic algal communities using a DNA metabarcoding approach for a portion of the plastid rbcL gene: samples from 19 sites from four of the Main Hawaiian Islands collected over two seasons were compared with previously published host selection data for P. cf. ianthobapsus, and filtered for A. lacerata detection. 41 new species and three novel lineages were discovered from 98 siphonous green algal OTUs recovered. Comparison of these OTUs with kleptoplast diversity studies revealed P. cf. ianthobapsus is a more specialized herbivore than previously reported. A. lacerata was confirmed as present beyond the islands of Kauai and Oahu, with three populations recovered from west Maui. Metabarcoding provides a powerful tool to explore community assemblages, particularly of diminutive and cryptic algal turf communities where invasive species are challenging to detect by traditional survey methods.