Tropical glaciers are rapidly disappearing, particularly in isolated mountain peaks below 5,000 m elevation. These glaciers are fundamental substrates for unique cryogenic ecosystems in high tropical environments where the ice, melting water and rocky substrate sustain microbiological communities and other meso- and macro-biota. This study uses the Red List of Ecosystems guidelines to diagnose the collapse of the tropical glacier ecosystem of the Cordillera de Mérida, Venezuela. We undertook the assessment with existing estimates of glacier ice extent, indirect historical estimates of ice mass balance and global mechanistic models of future ice mass balance. We complemented these with additional statistical analysis of trends and bioclimatic suitability modelling to calculate and predict rates of decline and relative severity of degradation in selected ecosystem indicators. The evidence suggests an extreme risk of collapse (Critically Endangered) because of a prolonged and acute reduction in ice extent and changes in climatic conditions that are leading to the complete loss of ice mass. The ice substrate has declined 90% in the last 20 years, and observed acceleration of the rate of decline suggests it will probably disappear within the next 5 years. Loss of ice substrate will trigger an immediate loss of supraglacial, englacial and subglacial biotic compartments and initiate a decades-long succession of forefield vegetation. However, ongoing inventories of native biota and monitoring of ecosystem transitions can provide valuable insights and lessons for other ecosystems facing similar risks. The Red List of Ecosystems assessment protocol provides a useful framework for comparative analysis of cryogenic ecosystems.