Chrysophycean stomatocyst assemblages were analysed from the sediments of 17 lakes and ponds from Svalbard as one component of a multi-proxy investigation of recent environmental change in the high Arctic. Sediment cores and water chemistry were collected from each of the study lakes, and chrysophyte stomatocysts were investigated from the top 0.25 cm of sediment (present-day) and bottom (i.e. bottom of short sediment core, pre-industrial) sediment samples. This study represents the first undertaking of chrysophyte cyst morphology and distribution on Svalbard. A total of 153 cyst morphotypes were described with light microscopy and/or scanning electron microscopy, of which 21 are new forms.Canonical correspondence analysis indicates that the present-day distribution of cysts is significantly related to pH (p = 0.02), altitude (p = 0.02), and Na + (p = 0.04). Marked shifts in chrysophyte cyst assemblages were recorded between the top and bottom sediment samples of most lakes. Rose et al. (2004) have demonstrated that Svalbard lakes receive atmospheric contaminants from both local and remote sources. The observed assemblage shifts may be the result of the combined effects of these point sources and long-range pollutants, or the effects of recent climate change, or both.