© 2018, © 2018 Taylor & Francis Group, LLC. Physiological synchrony within a dyad, or the degree of temporal correspondence between two individuals' physiological systems, has become a focal area of psychological research. Multiple methods have been used for measuring and modeling physiological synchrony. Each method extracts and analyzes different types of physiological synchrony, where ‘type’ refers to a specific manner through which two different physiological signals may correlate. Yet, to our knowledge, there is no documentation of the different methods, how each method corresponds to a specific type of synchrony, and the statistical assumptions embedded within each method. Hence, this article outlines several approaches for measuring and modeling physiological synchrony, connects each type of synchrony to a specific method, and identifies the assumptions that need to be satisfied for each method to appropriately extract each type of synchrony. Furthermore, this article demonstrates how to test for between-dyad differences of synchrony via inclusion of dyad-level (i.e., time-invariant) covariates. Finally, we complement each method with an empirical demonstration, as well as online supplemental material that contains Mplus code.