Fluorescence microscope images showing the position of the chloroplasts (red) and the nucleus (blue). The positions of these organs determine what species the cell belong to. (University of Tasmania)

Two new types of toxic algae found to be killing fish in the Southern Ocean, could affect sustainable fishing levels.

A University of Tasmania scientist, Dr Miguel de Salas says microscopic samples taken over the last two years show the algae is abundant and when in bloom, produces a distinctive red-coloured tide.

He has discovered fish are suffocating from the algaes, and says this means sustainable fishing level calculations are probably wrong.

"If this algae has not been taken into account when working out what the primary production is and what a sustainable fishery is, it means we are probably over-estimating how much we can fish," he said.

"Which would mean we're running the risk of over fishing unless we are taking the fish into our calculations."