Seven bays and four streams were sampled for surface floating pupal exuviae of Chironomidae (Insecta: Diptera) from the Lake Hovsgol watershed, Mongolia in July of 1997. A total of 52 taxa were identified with 12 species being new records for Mongolia and 1 species being a new record for the Lake Hovsgol Region. Communities of emerging chironomidae were compared between lake bay and lake affluent stream environments to determine whether affluent stream chironomids were recruited in the ultra-oligotrophic lake bays. Hierarchical cluster analyses were used to classify sites for this comparison. Bays and streams were classified together based on physical and habitat data, but formed distinctly different classes based on the chironomid community data. These two classification schemes were incongruent at a correlation of -.01. Stream sites and bay sites were comprised of either rheophilic or limnophilic chironomid communities, respectively, resulting in their separate classifications. One bay site located near Hatgol, a small town at the southern tip of Lake Hovsgol, was unique because it was composed of chironomids tolerant to elevated concentrations of organic waste.