Ichthyoliths — microfossil fish teeth and shark dermal scales (denticles) — are found in nearly all marine sediments. Their small size and relative rarity compared to other microfossil groups means that they have been largely ignored by the paleontology and paleoceanography communities, except as carriers of certain isotopic systems. Yet, when properly concentrated, ichthyoliths are sufficiently abundant to reveal patterns of fish abundance and diversity at unprecedented temporal and spatial resolution, in contrast to the typical millions of years-long gaps in the vertebrate body fossil record. In addition, ichthyoliths are highly resistant to dissolution, making it possible to reconstruct whole fish communities over highly precise and virtually continuous timescales. Here we present methods to isolate and utilize ichthyoliths preserved in the sedimentary record to track fish community structure and ecosystem productivity through geological and historical time periods. These include techniques for isolation and concentration of these microfossils from a wide range of sediments, including deep-sea and coral reef carbonates, clays, shales, and silicate-rich sediments. We also present a novel protocol for ichthyolith staining using Alizarin Red S to easily visualize and distinguish small teeth from debris in the sample. Finally, we discuss several metrics for quantification of ichthyolith community structure and abundance, and their applications to reconstruction of ancient marine food webs and environments.