Bryophytes live in a diverse array of habitats from blazing deserts to arctic tundra. They can also occupy habitats ranging in moisture level from terrestrial to partially aquatic to completely submerged. Often when species move into aquatic habitats they lose morphological features, which can make it challenging to elucidate evolutionary relationships based on morphology. Species in the moss genus Fissidens reside in habitats across a range of moisture levels from terrestrial to aquatic. In this study our aim was to determine the evolutionary relationships between fully aquatic Fissidens species, including members of Subgenus Octodiceras, Section Sarawakia, and Fissidens brachypus, a species that grows exclusively on amazonian sponges. In order to address this aim, we conducted a molecular phylogenetic study using data generated from herbarium specimens. A total of 27 species were sequenced and analyzed, 12 of which are fully aquatic.  Using a probe set for target enrichment (GoFlag408), we recovered hundreds of loci for each specimen, including a specimen collected in 1842. The resulting sequences were put through a multi-step pipeline in which we (i) trimmed the raw reads, (ii) assembled the targeted loci, (iii) probe trimmed, (iv) inferred orthology with reference genomes, (v) filtered contaminants, and (vi) aligned and merged isoforms. Post-processing scripts were run in order to prepare the resulting files for further analysis including file conversions, alignment pruning, and file concatenation. The resulting sequences were used to build two trees: a concatenated Bayesian Inference tree using MrBayes and a coalescent-based tree using RAxML and ASTRAL. Using the resulting trees, we determined how many times these species have transitioned to aquatic habitats across the genus Fissidens. Studies like this enable us to expand our understanding of habitat transitions and morphological evolution across plants.