ABSTRACTThe dynamics of chrysophyte populations and the onset of encystment in relation to several physical, chemical, and biological variables were studied in two Canadian lakes, Lake Opinicon (LO) and Upper Rock Lake (URL). LO is shallow and polymictic during the ice‐free season, whereas URL is deep and dimictic. Seasonal patterns of many limnological variables, as well as species composition and seasonal dynamics of chrysophyte assemblages, were broadly similar in both lakes. Three groups of chrysophytes were recognized: 1) taxa that were more abundant during ice cover and/or early spring and occasionally in late fall(Dinobryonspp. Ehrenberg andSynura spinosaKorsh), 2) taxa that seemed to prefer moderately warm waterproglena americanaCalkins andOchromonassp. Wyssotzki) and had maximum densities in late summer and occasionally in the fall, and 3) taxa that occurred in low numbers and did not exhibit any discernible seasonality in the two lakes(Mallomonasspp. Perty). Encystment rarely occurred during ice cover in both lakes. Stomatocyst concentrations were highest shortly after ice breakup (late April or early May), declined to trace levels by June, and remained at those levels until the end of the sampling season(late November). Encystment rates (cyst concentrations) were higher in dimictic URL. Encystment in both lakes coincided with concurrent changes in physical and chemical variables and chrysophyte vegetative cell densities, but it was not possible to pinpoint the exact conditions responsible for triggering encystment. Only a small proportion of chrysophytes encysted. Cyst production within a lake may vary from year to yea