This study investigates the epilithic diatoms from the Dolores and Laja Rivers, located within the Upper Laja River Basin, Guanajuato, Mexico. The samples were collected during the cold-dry (January) and rainy (October) seasons of 2011. One-hundred seventy three infrageneric taxa were identified, 7 of which are new records for Mexico: Fallacia monoculata, Hantzschia abundans, Navigiolum uruguayense, Neidium bisulcatum, Nitzschia solita, Planothidium incuriatum and Sellaphora bacilloides; it is worth mentioning that Navigiolum is a new record at the genus level. Furthermore, 3 species are new records for the state of Guanajuato: Gomphonema laticollum, G. subclavatum and Gomphosphenia lingulatiformis. Teratological forms of 6 species were also found in the sampling sites with higher nutrient concentrations, with relative abundances varying from 0.8 to 8.3%.