Family Azollaceae has seven species with a controversial taxonomy. The identification of species without reproductive structures relies on vegetative characters but some are variable, leading to misinterpretations. The molecular methods may be helpful, but until now, they did not provide a conclusive Azolla taxonomy. Therefore, we studied the family Azollaceae at vegetative and molecular levels. Analysis of vegetative, random amplified polymorphic DNA (RAPD) and combined data showed a comparable grouping of the Azolla species in two main clusters: cluster I, referred to as section Rhizosperma (A. pinnata and A. nilotica) and cluster II, referred to as section Azolla (A. filiculoides, A. microphylla, A. caroliniana and A. mexicana), with the exception of A. rubra, which clustered differently depending on the method. All the Azolla species were distinguished by the 13 polymorphic vegetative characters, the 211 RAPD markers or the combined data, with the latest showing the highest discrimination. The Shannon Index diversity was greater with RAPD (2.276) than with vegetative characters (0.054), highlighting the higher discriminating power of the molecular data. The partitioning of diversity was, as expected, high among species for all the types of data and low within species, with the lowest diversity obtained for morphological data. Both data sets (vegetative and RAPD) allowed the distinction of all the species and their clustering into sections Rhizosperma and Azolla, suggesting this as the most correct for this family. The dendrogram from the combined data was the most accurate, highlighting the benefit of integrating different types of data to study the family Azollaceae.