We explored the frequency response of krill target strength (TS) to understand the Antarctic krill (Euphausia superba) and ice krill (Euphausia crystallorophias) using the stochastic distorted-wave Born approximation (SDWBA) model. The results showed that the distribution of orientation and the fatness factor could significantly impact on the frequency response of TS. Krill TS is clearly depended on acoustic properties, which could affect to estimate the biomass of two krill species. The results provide insight into the importance of understanding TS variation to estimate the Antarctic krill and ice krill biomass, and their ecology related to the environmental features in the Southern Ocean.