In the tropical and subtropical regions, there is a large number of species which has not been yet described. The high possibility of extinction makes their inventory a priority. In this paper, 23 diatoms taxa from Andean lotic systems and lentic waterbodies localized in the Departments of Antioquia, Santander and Chocó, Colombia, are analyzed with light and scanning electron microscopy. Each taxon is described and information about environmental characteristic of the sites where they were collected and distribution in Colombia is given. The studied taxa belong to the orders Thalassiosirales (1), Aulacoseirales (1), Fragilariales (4), Cymbellales (7), Achnanthales (2), Naviculales (7), and Thalassiophysales (1). Fifteen of them are recorded for the first time in Colombia and Encyonema jemtlandicum in South America. A comparison with the diatom flora of the Colombian Amazonia showed that there were only three taxa in common to these two equatorial regions probably due to the influence of altitudinal gradient.