An agricultural country, Pakistan is highly dependent on the Indus irrigation system, one of the largest irrigation networks in the world. The Indus River catchment area upstream of Tarbela reservoir is called the Upper Indus River basin (UIB) which contributes the main inflow to the main course of the Indus River at high elevations as a result of snow and glacier melt. A large portion of the UIB is situated in the remote regions of Hindukush-Karakoram-Himalaya ranges. Seasonal variation of the snow and glacier cover influences directly the stream flow in the Upper Indus River. It is, therefore, important to monitor the seasonal snow cover in snow-fed catchments for several purposes such as hydrometeorology, flood forecasting and water resource management. The hydro-meteorological and snow cover investigations based on the ground data are very difficult in these regions. Satellite remote sensing is a powerful tool to estimate the snow and glacier (cryosphere) covered area in remote and inaccessible areas. MODIS snow cover products have been widely used to estimate the snow cover area by researchers (Maurer et al., 2003; Tahir et al., 2011; Tekeli et al., 2005) in several regions of the world. MODIS (MOD10A2) snow cover satellite product over a period of 12 years (2000 to 2011) will be used to estimate the snow and glacier cover trend in the Gilgit River basin (a sub-catchment of the UIB). Gilgit River basin nearly doubles the Indus River flow at Partab bridge so the snow cover estimation will help the water managers to manage the water resources in the UIB.