In the course of research performed in the continuous and discontinuous permafrost zone of the north of Western Siberia, the values of autotrophic (root) and heterotrophic (microbial) soil respiration and their ratio were estimated for typical ecosystems of the area. The data were obtained on the basis of a complex of field, laboratory, and calculation methods: shading, the root exclusion technique (comparison of emissions at similar sites with and without vegetation), the method of component integration or separate incubation, and the regression method. For soils of plateau palsa, the root contribution to total soil respiration was 16–30% with the use of the shading method and 14 ± 6% under the application of the component integration method. The contribution of root respiration was 60% for soils of shrub–green-moss pine forests and 30% for lichen pine forests. It may be assumed that, in forest ecosystems of the studied area, the contribution of root-derived respiration is even higher, which is related to the undercounting of respiration of tree roots and/or of rhizomicrobial microorganisms and priming effect by some methods. The contribution of root respiration in soils of mound palsa averaged 40%. For tundra with frost-boil ecosystems, the variation in the contribution of root respiration was 15–70%, depending on the location on microelements of cryogenic topography (boils and interboils). All the methods are characterized by disadvantages and some assumptions. These require additional studies to check or correct the data. The interpretation of the results is not always obvious. When using different techniques, similar results were obtained at a large number of replications of experiments during several seasons. The work also presents data on the absolute values of the specific root respiration for different species and size fractions, the value of the root biomass, and the microbial respiration of soils of different permafrost landscapes.