TheSetophaga petechiacomplex includes 43 subspecies distributed within the new world, of which some are migratory and others are resident, with only two resident subspecies in the Mexican Caribbean:Setophaga petechia bryantia mangrove subspecies belonging to theerithachoridesgroup resident on the mainland of the Yucatan Peninsula andSetophaga petechia rufivertexendemic to Cozumel Island and belonging to thepetechiagroup. Recently, a new population of individuals presenting intermediate phenotypic traits and living in mangrove ecosystems was discovered and reported for Cozumel Island. In this study, we used a multi-character approach including genetic (five ISSR genetic markers), morphometric (eight traits), phenotypic (four characteristics of males), and acoustic dataset (11 parameters) to understand the process of differentiation and the status of these new island individuals in relation to the two well-established subspecies using a total of 60 individuals (20 for each group). Through multivariate analyses based on different dataset used in our study, we show how the new population is related to the endemic island subspecies,S.p.rufivertexand to the mainland subspecies,S.p.bryantiwhile demonstrating finite differences. We conclude that the new population ofS.petechiaon Cozumel Island is a well-established population with high level of differentiation.