The spatial pattern of glacial retreat in Central Asian highlands are more intensive in last decades and impact on water resources are noteworthy in arid regions of Kyrgyz Republic. This research is an effort to assess the recent glacial retreat in Chon and Kichi Naryn catchments. The study conducted for period of 45 years (1965-2010) using 1:25000 scale topographic maps and ALOS/AVNIR satellite imagery shows that glacier area decreased by 21.3% in total. The dramatic changes have happened in south-facing glaciers than north facing glaciers with areal loss of loss of 23.6% and 19.8% respectively. The accelerated changes in glacial retreat will have compounding effect on shortage of water in densely populated areas and also increase in frequencies glacial induced hazards.