The delimitation of functional spatial units or functional territories is an important topic in regional science and economic geography, since the empirical verification of many causal relationships is affected by the size and shape of these areas. This paper proposes a two-step method for the delimitation of functional territories and presents an application for three developing countries: Mexico, Colombia and Chile. The first step of this method uses nighttime satellite images to identify the boundaries of urban continuums (conurbations). When these continuums extend over more than one municipality, we group and redefine them as a new single spatial unit. The second step calculates a dissimilarity index using bidirectional labor-commuting flows between the resulting areas of the first step and then applies a standard clustering procedure to delineate the definitive functional territories. Our results suggest that, using nighttime satellite images, our method can lead to a more accurate definition of functional territories, especially in developing or underdeveloped countries where the official data on labor-commuting flows are often outdated or unreliable.