This dataset on Zenodo contains the raw sequencing data for: La Spada et al. (2022) DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems. This a subset of 192 demultiplexed Illumina MiSeq raw sequencing samples run at the James Hutton Institute in January 2020, consisting of two 96-well plates labelled with the Illumina A and D multiplexing kits. There are 61 pairs of raw gzipped compressed FASTQ files (122 files), provided as a 930MB gzipped compressed tar-ball. From the D multiplexing kit, there are 27 Nature Reserve (NR) samples, 16 Botanical Garden (BG) samples, and 6 managed Citrus Orchard (CO) samples containing Phytophthora targeted ITS1 marker sequences, and 6 synthetic controls (prefix GL1D) which should have contained only four known synthetic sequences. Additionally included are the 6 synthetic controls (prefix GL1A) from the A multiplexing kit, which were clean. The filenames start with the sample name, followed by something like DH03_S183_L001_R1_001.fastq.gz where DH03 indicates well H03 on the 96-well plate labelled with the D multiplexing set, S183 is the MiSeq sample number (from 1 to 192), and R1 (or R2) indicate the Illumina forward (or reverse) paired read files.