Microalgae of Bacillariophyta phylum from continental waterbodies and watercourses of Azerbaijan have been inventoried for the first time. The list of diatom algae represented 381 taxa (443 infraspecies taxa) which belong to the 84 genera, 36 families, 16 orders, 6 subclasses and 3 classes according to the latest taxonomic arrangements was made. The level of the study, distribution and taxonomic specifics of diatoms in large physiographic areas of the country are discussing.