Capelin (Mallotus villosus) is both an important commercial and ecological resource of the North Atlantic subpolar region. Two decades ago, the stock distribution around Iceland drastically changed. During autumn, which corresponds to the main feeding period, the capelin stock was previously located between the North of Iceland and the Jan Mayen area. Since the beginning of 2000s, the feeding aggregation has been located at the east coast of Greenland, inducing slight changes in the timing and route of the capelin spawning migration along the Icelandic shelf, and therefore in the catches. Changes in the distribution of capelin around Iceland made it both more difficult and expensive to assess the distribution of the stock with current survey methods. Here, we compare environmental DNA (eDNA) data to the acoustic data collected during the autumn monitoring survey, which leads to a preliminary estimate of the stock size. eDNA samples were collected at five different depths and were analyzed both horizontally across latitudes and longitudes and vertically across depth profiles. We detected eDNA in most of the locations where acoustic data detected capelin. Generalized linear models suggested that eDNA concentrations can be used as a proxy for the detection and quantification of capelin. The horizontal distribution of eDNA observed during both years corresponds with the horizontal distribution of capelin registered with the acoustic approach, while the vertical distribution indicates both effects of oceanic currents and diel vertical migration on eDNA detection and quantification.