To address the global biodiversity crisis, standardized data that are rapidly obtainable through minimally invasive means are needed for documenting change and informing conservation within threatened and diverse systems, such as coral reefs. In this data paper, we describe 18S rRNA gene amplicon data (V1–V3 region) generated from samples collected to begin characterizing coral reef eukaryotic community composition at the Palmyra Atoll National Wildlife Refuge in the Central Pacific Ocean. Sixteen samples were obtained across four sample types: sediments from two sieved fractions (100–500 μm, n = 3; 500 μm-2 mm, n = 3) and sessile material scrapings (n = 3) from Autonomous Reef Monitoring Structures (ARMS) sampled in 2015, as well as seawater from 2012 (n = 7). After filtering and contaminant removal, 3,861 Amplicon Sequence Variants (ASVs) were produced from 1,062,238 reads. The rarefaction curves demonstrated adequate sampling depth, and communities grouped by sample type. The dominant orders across samples were polychaete worms (Eunicida), demosponges (Poecilosclerida), and bryozoans (Cheilostomatida). The ten most common orders in terms of relative abundance comprised ~60% of all sequences and 23% of ASVs, and included reef-building crustose coralline algae (CCA; Corallinophycidae) and stony corals (Scleractinia), two taxa associated with healthy reefs. Highlighting the need for further study, ~21% of the ASVs were identified as uncultured, incertae sedis, or not assigned to phylum or order. This data paper presents the first 18S rDNA survey at Palmyra Atoll and serves as a baseline for biodiversity assessment, monitoring, and conservation of this remote and pristine ecosystem.
