Chrysophycean stomatocysts associated with three different periphytic substrates (wet mosses, submerged mosses and rock scrapes) were investigated from ponds on Cape Herschel (78°37'N, 74°42'W), Ellesmere Island in the Canadian High Arctic. The goal of this study was to determine whether a distinct assemblage of periphytic chrysophyte cysts existed and, if so, whether assemblage composition varied with substrate and between ponds. One hundred and thirty-seven different cyst morphotypes were observed with light microscopy from 68 periphytic samples taken from 35 ponds. Twenty-six of these cysts were new morphotypes, of which 16 were identified and described using scanning electron microscopy. Significantly more cyst types with collars and hooked projections in the collar region (i.e. ‘hooked’), and fewer unomamented morphotypes were recorded in the periphytic habitats as compared to the surface sediments. Wet moss stomatocyst assemblages were particularly distinct, with a high number of heavily silicified and hooked morphotypes. The morphotype richness was far greater in periphytic environments, with 86, 100 and 95 morphotypes observed in the wet mosses, submerged mosses and rock scrapes, respectively, as compared to only 35 types in the surface sediments of the ponds. Canonical correspondence analysis indicated that measured water chemistry did not account for the variation in the species data (paxic 1 < 0.01, 999 Monte Carlo permutations). This study suggests that distinct periphytic assemblages exist, and that cyst morphotype composition and richness varies with substrate.