Collecting acoustic data from fishing vessels is an important trend in fishery resources study, yet the quality of the data may be seriously compromised by inter-instrument acoustic interferences due to the lack of signal synchronization apparatus for onboard acoustic instruments. In order to fully use the contaminated acoustic data, a method of extracting swarm signals from echogram with strong interference was established based on the relevant modules in the Echoview,an acoustic data post-processing software. The methods were then applied to the acoustic data on Antarctic krill collected onboard a fishing vessel operated around South Orkney Islands during February 2011, and the interference was effectively removed from the echogram. Distinct diel vertical migration was observed in the krill swarms. The geometrical center of the krill swarms was distributed in layers with a mean depth of 77.4 m and a mean thickness of 41.2 m in daytime, while the swarms tended to migrate upward nocturnally at a mean depth of 34.9 m and a mean thickness of 8.8 m.