Azolla is a small floating fern, with both sexual and non-sexual reproduction. In the life cycle of plants, transition from vegetative to reproductive stage is a key step and controlled by genetic factors. Floral development in flowering plants regulated by a network of regulatory genes, which are stimulated by environmental factors such as day length, quality of light and temperature that lead to transitions from vegetative to reproductive phase. The MADS-box gene is the family of a transcription factors that determines the floral organs in flowering plants. This gene family identified by MADS domain that bind to DNA. MADS-box genes are important regulators of development and differentiation. To more study of MADS-box genes in ferns as well as a better understanding of the relationship between these genes, three genes including SOC1 , LFY and CAL were studied in Azolla . The sequence analysis of these genes showed that the amino acid sequences of the MADS genes in Azolla have a high homology with the MADS-box proteins in other non-vascular plants. Based on the phylogenetic analysis, three MADS genes isolated from A. filiculoides may belong to a new group of MADS genes in ferns. To understand the phylogenetic relationship between Azolla sample collected from Anzali wetland, we used the ITS sequences to determine the species type. The results revealed that the Azolla collected from the Anzali wetland originated from A. filiculoides . Key words : Azolla fern, MADS-box genes, SOC1 , LFY and CAL genes , ITS