This is the MiSeq data used for the project titled 'Insight into the diet of early stages of mesopelagic fishes in the Indian Ocean using DNA metabarcoding'.</p><p>https://doi.org/10.1016/j.dsr2.2024.105426</p><p>; PLEASE NOTE: each sample has 2x fastq paired-end files (metadata file), filenames 1 (R1) and 2 (R2) are for Leray and Zhan primer sets (pooled), and filenames 3 (R1) and 4 (R2) are for Lobo In this study, we apply DNA metabarcoding (18S rRNA and COI) to gut contents from Stomiiformes and Myctophiformes species from 20 sampling stations covering 30 degrees of latitude on the 110 degrees E meridian in the Indian Ocean. In total, 174 fish specimens from 13 genera were examined. Differences in the gut contents among fish families, geographic areas and fish stages were identified. Specimens within the family Myctophidae had the most diverse diet, more so in the northern sampling stations than the south. Gonostomatidae had the least diverse diet. Overall, the most frequently identified prey items from the gut contents were calanoid copepods and halocyprid ostracods. The proportion of halocyprids were also identified to be significantly different among Myctophidae larvae and juvenile specimens, which is a potential ontogenic shift in diet towards a higher ostracod contribution in juveniles as mouth gape increases. In comparison with other plankton abundance data, Copepoda were the most abundant plankton in the gut contents of all fishes sampled throughout the latitudinal gradient, allowing them to be a potential food resource through the region. There are indications that other less abundant plankton, such as like Ostracoda and Malacostraca, may be preferentially targeted by some mesopelagic fish families.