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Temporal distributions of Antarctic krill (Euphausia superba) density and aggregation types were characterized and compared using Nortek Signature100 and SIMRAD Wideband Autonomous Transceiver (WBAT) upward-looking echosounders. Noise varied between the two echosounders. With the Signature100, it was necessary to correct data for background, transient, and impulse noises, while the WBAT data needed to be corrected for background noise only. For selected regions with no visible backscatter, the signal-to-noise ratio of Sv values (i.e. the ratio between the signal and the background noise level) did not vary between the two echosounders. Surface echo backscatter was similar during similar time periods. Descriptive metrics were used to quantify spatial and temporal krill vertical distributions: volume backscatter, mean depth, center of mass, inertia, equivalent area, aggregation index, and proportion occupied. Krill backscatter density differed between the two instruments but was detected at similar mean depths. Krill aggregations were identified at each mooring location and classified in three types based on morphological characteristics. Each type of aggregation shape differed at the two spatially separated moorings, while the acoustic density of each aggregation type was similar. The Signature100 detected a lower number of krill aggregations (n = 133) compared to the WBAT (n = 707). Although both instruments can be used for autonomous deployment and sampling of krill over extended periods, there is a strong caveat for the use of the Signature100 due to significant differences in noise characteristics and krill detection.