An ecological analysis of wetlands in the high mountain jalca above 3700 m elevation in the Andes near Cajamarca, Peru, indicated that most wetlands are groundwater-supported peat-accumulating fens. The floristic composition of fen communities was controlled largely by groundwater chemistry, which was highly variable and influenced by watershed bedrock composition. Watersheds with highly mineralized rock discharged water as acidic as pH 3.7, which was high in CaSO4, while watersheds with limestone, marble, and skarn produced groundwater as basic as pH 8.2 and high in CaHCO3. Of the 125 plots sampled in 36 wetland complexes, >50% of plots had at least 3 m of peat, and 21 plots had peat thicker than 7 m. Most soil horizons analyzed had 18 to 35% organic carbon, indicating high C storage. A total of 102 vascular plants, 69 bryophytes, and 10 lichens were identified. Study plots were classified using TWINSPAN into 20 plant communities, which were grouped into four broad categories by dominant life form: (1) cushion plant communities, (2) sedge- and rush-dominated communities, (3) bryophyte and lichen communities, and (4) tussock grass communities. Direct gradient analysis using canonical correspondence analysis indicated that Axis 1 was largely a water chemistry gradient, while Axis 2 was a complex hydrology and peat thickness gradient. Bryophytes and lichens were more strongly separated in the ordination space than vascular plants and were better indicators of specific environmental characteristics.