Motile magnetotactic bacteria are normally separated from a solution by applying a low intensity (mT) orientating magnetic field. This constrains the bacteria to swim in the required direction. High gradient magnetic separation (HGMS) is a well established method for the extraction of magnetic particles from solutions. This paper reports on the separation properties of both motile and non-motile magnetotactic bacteria using both techniques. A comparison of HGMS separation with low field orientational magnetic separation is made and the conditions under which HGMS becomes beneficial are considered.