Botrychium oneidense is most often confused with B. multifidum and B. dissectum. In B. multifidum the leaf segments are about the same size and shape. It often occurs with B. dissectum which is more common and occurs in more diverse habitats. Blanch., and B. dissectum Spreng. Leaves of B. oneidense begin to develop in May and sporangia mature in late September.
Leaves persist through the winter and usually remain green.
The plants are tolerant of human disturbances such as lumbering as long as some trees are left to provide shade. It is highly probable that B. oneidense no longer occurs at many of these historic sites that are in areas where suburban development has occurred. Many other sites, however, are in areas where suburban development may have destroyed the habitat. Many historic localities are in or near fast-growing suburban communities. Alteration of the water regime also is a threat.