Abstract The morphological structure, size-age variability and dynamics of age-related fertility of producers of Baikal omul of pelagic, near-bottom and coastal morpho-ecological groups during the depressive state of the population were studied. There is an improvement in the indicators of the growth rate of fish, maturation and an increase in absolute individual fertility against the background of the dilution of the population and the release of the feeding area. A comparative characteristic of some morphological features of fish among morphological-ecological groups is given. The number of gill rakers on the first gill arch significantly distinguishes different morpho-ecological groups and ranges from 36 to 43 pieces for the near-bottom, from 40 to 46 pieces for the coastal and from 44 to 53 pieces for the pelagic morpho-ecological groups. It is noted that the spawning populations of the coastal and pelagic groups are mainly represented by young individuals. With age, the proportion of females increases in all groups. The largest indices of the pectoral, abdominal and anal fins, responsible for movement in the vertical plane, rotation and stop, are noted in the near-bottom group.