• Overgrazing by yaks & cattle
  
• Hunting & Poaching
• Extraction Of Timber & Fuelwood
• Unplanned Development
• Garbage accumulation
• Bio-piracy

The unique habitats within the Khangchendzonga Landscape are increasingly under threat as they undergo rapid transformation and alteration. Human disturbances such as firewood extraction, fodder lopping and cattle grazing have increased during the last two decades due to growth in tourism and population.

The primary direct threats to the area's unique biodiversity are land conversion and degradation, and landscape fragmentation. Over the last few decades, there has been a visible change in terms of landscape, species composition and density in studied forests. Key activities including grazing (local and trans-boundary activities across the border between India and Nepal) and associated fuel wood removal, tourism, selective forest product removal (for cash, subsistence, especially fuel wood, and tourism) and, to a lesser degree, wildlife hunting and poaching, in the Khangchendzonga Biosphere Reserve.

Within the buffer zone of KNP, many species of plants and animals are facing threats from various activities.

Selective felling of trees for fuelwood and timber brought about decrease in abundance of preferred species such as Rani chanp (Michelia exelsa), Lapsi (Spondias axillaris), Mehel (Eriolobus indica) and Mandane (Acrocarpus fraxinifolius).

Over exploitation of high altitude medicinal plants also resulted in rarity for species such as Kutki (Picrorohiza kurrooa), Jatamansi (Nardostachys jatamansi), Bikhma (Aconitum ferox), Khokim (Bergenia purpurascens) and Chimphing (Heracleum nepalense).

Indiscriminate poaching in the past have led to a marked decline in the population of the Snow leopard (Uncia uncia), Red panda (Ailurus fulgens), Musk deer (Moschus moschiferrus), Blue sheep (Pseudois nayaur) and some pheasants such as Tragopan (Satyr tragopan) and Himalayan Monal (Lophophorus impejanus).

A further threat in Sikkim is private land under cardamom cultivation. Many of the agro-forestry techniques currently in use are unsustainable and result in gradual erosion of biological diversity. After initially clearing private lands and planting cardamom, farmers gradually convert the forests into single species forests as they remove a variety of tree species to allow light in and for use as fuel for drying cardamom pods. Over time, soil fertility erodes and genetic variability declines as farmers plant more and more vegetative stock from cuttings rather than from seed.