The analysis of species diversity has benefited from multiple methodological approaches that are changing not only the way we measure biodiversity, but also our general conceptualization of it. We review the concepts and methods for measuring species diversity, including a report on how species diversity has been measured in tropical ecosystems, and summarize current methodological approaches that can be used to achieve more comprehensive analyses of species diversity. We reviewed papers dealing with species diversity published in Biotropica over the last 28 yr. Most of the studies were carried out in the Neotropics. The most popular methods for reporting alpha diversity were species accumulation curves, rarefaction curves, and the Shannon-Wiener index, while beta diversity assessments mainly relied on the Sørensen, Jaccard or Bray-Curtis indices. We offer a general framework for comprehensive biodiversity assessments that includes the alpha and beta components, and taxonomic, functional, and phylogenetic dimensions. We briefly describe the conceptual background, relevant methods, and examples of the components, and dimensions described in this framework. To improve our knowledge of tropical biodiversity and its regulatory processes, we encourage researchers to carry out more complete assessments, and to take advantage of the wide variety of methods available; methods that are perhaps especially useful in human-disturbed and human-managed landscapes.Abstract in Spanish is available with online material.