The southern Yucatan Peninsular Region project was designed from the outset as an integrative, multidisciplinary program of study examining tropical deforestation in the largest track of seasonal tropical forest remaining in Mexico and in which smallholder agriculture and a major biosphere reserve are juxtaposed in regard to land uses and covers. Treating land as a coupled human-environment system, the project joins the remote sensing, environmental, social, and modeling sciences in a way that is now recognized as land change science. This paper introduces the project, the study region, and six papers that explore some of the coupled system dynamics in the region. These include the sub-regional variation in deforestation, the pan-regional adoption or anticipation of cattle ranching, the emergence of divergent household agricultural and overall livelihood strategies, the roles of cultural and household histories in agricultural livelihood choices, the temporal intensification of swidden cultivation and its implications for forest species, and carbon stocks across cultivation units, including a new econometric modeling application to forecast changes in these stocks.