In previous work we have proposed an alternative index to Conapo, this index shows whether the marginalization of the municipalities has improved or deteriorated, and also has the characteristic of being highly correlated with it. In this paper we present the results of a longitudinal analysis of an alternative index to study the trajectories of marginalization at the municipal level between 1990 and 2010. The strategy analysis uses latent growth curves for longitudinal data applied to municipalities and shows the evolution of marginalization in the period considered. The resulting trajectories are classified using latent class analysis. The results indicate three types of linear trajectory classes: i) the first group formed by municipalities in 1990 with high deprivation index that experience a moderate but sustained growth towards the end of 2010; ii) a second group composed of municipalities whose trajectories started in 1990 with average levels of marginalization that fell to a moderate five-year rate; iii) the third group, with a clear predominance urban municipalities consists of municipalities with low marginalization index that decreased rapidly. These results show that in the last four data points a local convergence process has not taken place, but on the contrary one of territorial divergence. This information will enable to enrich the criteria for the distribution of resources allocated to these political and administrative divisions, help refine territorial targeting of existing social programs and may be used to guide new allocation of programs.