Below is a working checklist of Mount Desert Island's lycophytes. Please send corrections and updates to info@vfthomas.com. Photographs are welcome. Thank you.
| Family | Genus | Specific Epithet | authority | Sub-specific Epithet | authority | common name or hybrid formula | Sources (full citations given after this table) |
| Huperziaceae | Huperzia | appressa | (Desv.) A. & D. Love |   |   | mountain firmoss | Greene et al. (2005) |
| Huperziaceae | Huperzia | x protoporophila | A. Haines |   |   | H. appressa x H. lucidula | Haines (2003) |
| Isoetaceae | Isoetes | acadiensis | Kott |   |   | Acadian quillwort | Greene et al. (2005) |
| Isoetaceae | Isoetes | echinospora | Durieu | ssp. muricata | (Durieu) A. & D. Love | spiny-spored quillwort | Greene et al. (2005) |
| Isoetaceae | Isoetes | x harveyi | A. A. Eat. |   |   | I. lacustris x I. tuckermanii | Greene et al. (2005) |
| Isoetaceae | Isoetes | lacustris | L. |   |   | lake quillwort | Greene et al. (2005) |
| Isoetaceae | Isoetes | prototypus | D. M. Britt. |   |   | prototype quillwort | Greene et al. (2005) |
| Isoetaceae | Isoetes | tuckermanii | A. Braun ex Engelm. |   |   | Tuckerman's quillwort | Greene et al. (2005) |
| Lycopodiaceae | Dendrolycopodium | dendroideum | (Michx.) A. Haines |   |   | prickly tree clubmoss | Greene et al. (2005) |
| Lycopodiaceae | Dendrolycopodium | obscurum | (L.) A. Haines |   |   | flat-branched tree clubmoss | Haines (2003) |
| Lycopodiaceae | Diphasiastrum | tristachyum | (Pursh) Holub |   |   | blue ground-cedar | Greene et al. (2005) |
| Lycopodiaceae | Lycopodiella | x gilmanii | A. Haines |   |   | L. appressa x L. inundata | Greene et al. (2005) |
| Lycopodiaceae | Lycopodiella | inundata | (L.) Holub |   |   | northern bog clubmoss | Greene et al. (2005) |
| Lycopodiaceae | Lycopodium | clavatum | L. |   |   | common clubmoss | Greene et al. (2005) |
| Lycopodiaceae | Lycopodium | lagopus | (Laestad. ex Hartm.) G. Zinserling ex Kuzeneva-Prochorova |   |   | one-cone clubmoss | Greene et al. (2005) |
| Lycopodiaceae | Spinulum | annotinum | (L.) A. Haines |   |   | interrupted clubmoss | Greene et al. (2005) |
| Selaginellaceae | Selaginella | rupestris | (L.) Spring |   |   | rock spikemoss | Greene et al. (2005) |