Ferns have historically lagged behind angiosperms in the availability of genomic resources, but such resources are starting to be developed.
Fern Nuclear Genomes
The full, annotated, nuclear genome sequences of the waterferns Azolla and Salvinia are in progress, and Blaine Marchant at the University of Florida is working on sequencing the nuclear genome of Ceratopteris richardii.
In addition, we have some low-coverage genome skimming data available, from the study of Wolf et al. 2015.
Much of the increase in fern genomic data available has been in the form of transcriptomes, many of which have been generated by the 1000 Plants Project (1KP). BLAST access to the 1KP transcriptomes is available here, and additional data are available upon request.
A list of available fern plastome sequences (sequences of the chloroplast genome) is available here.