The goal of his research is to understand the factors that govern the evolutionary dynamics of organismal diversification. Why are some groups morphologically diverse? Are there general laws or themes that can be used to explain the uneven distribution of diversity in physiological traits across lineages? Does morphological diversity always signal mechanical, functional, or ecological diversity? To address these questions, Alfaro works largely on marine fishes. His research approach is interdisciplinary and quantitative and crosses traditional boundaries among evolutionary morphology, molecular phylogenetics, and theoretical evolution. He identifies and quantifies organismal diversity using morphological and functional morphological techniques; constructs evolutionary trees and tests evolutionary hypotheses using phylogenetic statistical methods; and uses models of trait evolution to explore form-function dynamics.