Knowledge on the early life history, ecology, and biology of marine species is crucial for future projections of the resilience of coral reef ecosystems and for adequate management strategies. A fundamental component of population dynamics is the recruitment of new individuals, and in some marine populations, this may be a limiting factor. Recruitment peaks of coral reef fishes commonly occur during the warmer months of the year in many subtropical and temperate locations worldwide. In the Red Sea, very little is known about the influence of temperature on reproductive patterns of coral reef fishes and studies on recruitment are missing. The Red Sea is one of the hottest and most isolated tropical seas in the world. We hypothesized that sea surface temperatures (SSTs) during the Red Sea’s hottest season may exceed the optimum for successful recruitment of some coral reef fishes, which therefore has to occur during other, cooler seasons, unlike recruitment among coral reef ecosystems around the world. We identified taxa among fish recruits by matching mitochondrial DNA sequences (using COI, commonly known as “barcoding”) and assessed potential biological and environmental drivers of recruitment. We studied three reefs located along a cross-shelf gradient for 12 consecutive months in the central Red Sea to capture seasonal changes in biotic and abiotic parameters along this gradient. Our results indicated that recruitment peaks did not occur during the hottest SSTs for most taxa, especially at the hottest inshore and mid-shelf reefs, and identified fish recruitment to be mainly and strongly correlated with the biomass of planktonic invertebrates. Moreover, temporal patterns of fish recruitment differed within and among taxonomic families among the reefs.