Isothecium myosuroides is an abundant and taxonomically problematic moss that occurs in Europe and on the west and east coasts of North America. It has sometimes been split into two taxa, I. myosuroides on the east coast of North America and in Europe, and I. stoloniferum on the west coast of North America. Isothecium stoloniferum has four distinct morphological types known as the ordinary, julaceous, coarse, and pinnate morphs. The degree to which the morphotypes are genetically distinct versus ecologically determined has been debated as has the distinction between I. stoloniferum and I. myosuroides, resulting in conflicting taxonomic treatments. This study uses phylogenetic analyses of the trnL-trnF and trnG regions of the chloroplast genome to examine relationships among the two species and four morphotypes. Molecular phylogenetic analyses reveal that there is some genetic basis to the morphs of I. stoloniferum, and that I. stoloniferum is paraphyletic. Accessions of I. myosuroides form a trans-Atlantic monophyletic group. The remaining samples form two distinct groups that each include samples of two morphotypes within I. stoloniferum. Populations of julaceous and ordinary morphotypes form a monophyletic group. Populations of coarse and pinnate morphotypes form an unresolved polytomy at the base of the clade that includes accessions of I. myosuroides.