In this study, we combined microscopy data with long-read 18S rRNA gene amplicon data to investigate genetic variation within specimens and morphospeices of polycystine Radiolaria. The fastq files deposited here are the raw, unprocessed PacBio CCS data, as received from the sequencing facility. DNA sequences in each file belong to the target isolated radiolarian specimen listed in the metadata file, in addition to some sequences from prey, symbionts, or other organisms inhabiting the sampled environment.