The present study of chrysophycean cysts is based on 105 lakes from the Pyrenees selected from the about one thousand existing in those ranges. Sediment and water samples collected along four years 1984, 1995, 1996 and 1998 during the summer season. These lakes where chosen from among a thousand lakes to provide a broad range of environmental conditions. Two hundred morphotypes are described, eighty-two have not previous published description. The cyst morphotypes are illustrated with 464 images, 248 of them from scanning electron microscope. The ecological data are summarised in a individual table for each morphotype. This table shows the ecological optima and tolerances for various water chemistry components and preferences for lake in physical characteristics.