Northern Bog Clubmoss resembles a large moss. It has prostrate or arching stems that root at irregular intervals and give rise to erect branches that are up to 10 cm high. The narrow, pointed leaves are 4-8 mm long and clothe the stems and branches in 8-10 ranks. Each spore is subtended by a bract, or sporophyll, that is similar to the leaves and borne in dense spikes at the top of erect branches. It is difficult to distinguish the fertile and sterile portions of the branches.

Shell hard, somewhat flattened; bright yellow lines on head and limbs; lower shell orange or reddish, with conspicuous dark markings in juveniles; upper shell often with narrow yellow lines (reduced in larger individuals), less often with dark reticulation; upper jaw notched at tip; maximum upper shell length of female about 25 cm, rarely more than 21 cm (males are much smaller). Mature male: vent located beyond rear edge of upper shell with tail extended; fingernails very long; lower shell not concave.