The value of fluctuating asymmetry (FA) of trees and small mammals is considered as an indicator of developmental instability. The urban territories with recreation zones, sites with increased radiation background, and the areas affected by mining facilities have been analyzed as anthropogenically transformed areas. The following tree and small mammalian species are the objects of the study: Siberian silver birch (Betula platyphylla), spreading birch (B. divaricata), dwarf birch (B. exilis), shrub alder (Duschekia fruticosa), basket willow (Salix viminalis), northern red-backed vole (Clethrionomys rutilus), tundra vole (Microtus oeconomus), Laxmann’s shrew (Sorex caecutiens), and tundra shrew (S. tundrensis). In total, 60000 leaves have been measured and 3500 rodent sculls have been examined. The issues of selection of bioindicator species and the factors distorting the results of environmental quality assessment according to developmental instability are discussed. A statistically significant increase in FA of plants is recorded in urban territories as compared with the wildlife biotopes. A positive correlation of FA value with transport load, concentration of heavy metals in soil, and atmospheric air pollution is observed. The proximity to a roadway and the state of road pavement influence the FA value. The main source of pollution in the administrative center (Yakutsk) is motor vehicles; correspondingly, large streets and crossroads with a high transport load are the most polluted sites. As for the industrial center (city of Mirnyi), pollution spreads from the areas affected by mining to the residential area. The main pollution source in a small administrative center (city of Aldan) is the federal highway. It is recommended to concurrently use the FA characteristics of plant and animals in the area affected by the mining industry. Characteristic of this industry is withdrawal of large areas of natural landscapes; typically, transformed plots alternate weakly affected plots. The specific features of the effects of diamond, gold, and coalmining industries, as well as oil and gas field development, are discussed, which should be taken into account in sampling for bioindication. The problem of bioindication in the areas completely devoid of soil and plant cover can be solved by biotesting via assessment of bunching onion seed germination rate and the rate of mitotic aberrations. An increase in the FA level in trees and small mammals is observed in the areas transformed by the mining industry displaying a chronically increased radiation background and oil-polluted as a result of technogenic accidents. The use of FA index makes it possible to estimate the environmental quality and to compare the state of territories located under different natural and climatic conditions and influenced by multicomponent anthropogenic impacts differing in their strength and genesis, which interferes with their comparison.