Coral reefs are among the most degraded ecosystems worldwide, with declines in coral cover in excess of 80% and overfishing prevalent on the majority of reefs. Human activities have affected coral reef ecosystems for at least 1,000 years, and overfishing is typically the earliest human activity to impact coral reef environments. Thus, historical analyses of the effects of historical fishing are essential to assess changes that occurred before modern observations were made. My thesis assesses long-term change in a variety of species and ecosystems in the Caribbean region. I compiled documents from historical archives and other repositories, extracted ecological data, and developed methods to analyze these data. Across the wider Caribbean region, I found declines of more than 99% in green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) turtle populations and a severe reduction in nesting habitat. Next, I estimated historical population sizes for the Caribbean monk seal (Monachus tropicalis) to be 233,000 - 338,000 individuals, and determined that the prey biomass remaining in Caribbean reefs is insufficient to feed historical populations. I then focused on the sponge fishery in the northern Caribbean and determined that the population crash in several species of marine sponges (Spongia spp., Hippospongia spp.) in the first decades of the twentieth century was likely related to overfishing, and precipitated broader ecological and social changes. In the Florida Keys, I quantified declines of large bodied fish using historical photographs, and determined that the largest fish are 50% shorter today than fifty years ago. I then analyzed historical fishing records for the goliath grouper (Epinephelus itajara) and determined that this species was depleted several decades earlier than previously thought. Next, I assessed change for a variety of coral reef organisms over the last several centuries and determined that declines occurred at relatively low human population densities, and did not follow a pattern of fishing down the food web as has occurred in temperate and oceanic environments. Finally, I assessed historical reasons for the continuation of recreational fishing despite the severe degradation that has occurred. These results have conservation implications both at the species and ecological leve