Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by nitrogen isotope determinations of fern biomass and detection of N2O released. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct near full-length Rhizobiales genomes were identified from leaf-pocket enriched samples from ditch grown A. filiculoides. Annotation revealed genes for denitrification but not N2-fixation. 15N2 incorporation was active in ferns with N. azollae but not in ferns without. N2O was not detectably released from surface sterilized ferns with the Rhizobiales. N2-fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2O.