Niche differentiation is a key stabilizing mechanism in the maintenance of biodiversity and species coexistence. Recent work shows that trophic niche partitioning between parrotfishes (Labridae: Scarini) is more extensive than previously described. One Indo-Pacific species, Scarus spinus, appears highly specialized, scraping crustose coralline algae (CCA) with powerful oral jaws. CCA are of low nutritional value, suggesting that the dietary targets of this parrotfish are protein-rich microphotoautotrophs associated with CCA, particularly filamentous cyanobacteria. We collected feeding substrata samples at mid-shelf and outer-shelf sites near Lizard Island, Great Barrier Reef, Australia, in 2018 and 2019, respectively. Scarus spinus were followed on snorkel. When biting was observed, bite substrata were photographed and then a 22-mm-diameter core extracted around the bite site. Density of biota including filamentous cyanobacteria and diatoms was quantified microscopically on photographs of the bite cores (up to 630 × magnification). The taxonomy of cyanobacteria and CCA was refined using next-generation sequencing of 16S and 18S rRNA genes, respectively. CCA and filamentous cyanobacteria were present on all bite cores and the density of filamentous cyanobacteria where S. spinus fed did not vary between mid-shelf and outer-reef samples. Epiphytic and shallow endophytic cyanobacteria were consistently associated with the CCA where S. spinus fed, including Calothrix spp., Mastigocoleus testarum, Leptolyngbya spp., Hyella patelloides and Oscillatoriales. Our results emphasize the importance of high-resolution species-specific dietary data for parrotfishes. We conclude that polyphasic methods are essential both for diet tracing and to develop our understanding of the cyanobacteria that are integral to coral reef functioning.