Classical analysis of constraints and challenges associated with development in Latin American middle-income countries were done based on countries' per capita income levels. Since the first decade of the twenty-one century (CEPAL, 2012) the structural gap approach is an alternative criterion to that of per capita income. It identifies key areas where there are "gaps" that hamper their social and economic development (OECD, 2014); such as poverty, inequality, and social inclusion. In this article, we use hierarchical cluster analysis methods to study the socio-economic development of cities in Ecuador. The aim is to add depth and flexibility to study a more complex reality on the level of development inside a country. Therefore, from the resulting city taxonomy specific policies could be addressed to improve quality of live and sustainability of population.