The distribution of fish eggs and larvae (ichthyoplankton) reflects spawning and nursery areas as well as dispersal routes. This study’s goal is to demonstrate how the identification of ichthyoplankton species and stages and their spatial distribution among natural reefs (NRs) and artificial reefs (ARs) may serve as decision-making tools in conservation and fishery management. Natural reefs exhibited an eight-times higher abundance of eggs, as well as the highest abundance of larvae in the yolk-sac and preflexion phases. In contrast, ARs had the highest abundance of larvae in the flexion and postflexion phases. Natural reefs may serve as breeding grounds for Scaridae, Labridae, and Mugilidae; whereas, ARs may serve as breeding sites for Lutjanidae, Synodontidae, Carangidae, Fistularidae, and Haemulidae. Our study revealed differences between ARs and NRs, which demonstrate the potential of artificial reefs to expand the supply and settlement options of reef fishes and consequently can lead to increased fish production with potential benefits to adjacent fishing areas through connectivity. Thus, ARs as no-take sites can be effective tools for both fishery management and biodiversity conservation. The findings highlight the potential use of ichthyoplankton tools and the importance of considering both types of reefs in marine conservation and management efforts.