The use of Environmental DNA (eDNA) in monitoring ecosystems is now gaining attention in the field of research. The technique has shown a snapshot of the organisms present in the ecosystem being studied. Recent studies have demonstrated that the distribution and biomass of aquatic organisms can be estimated through detection and quantification of eDNA samples in the studied ecosystem. The approach is very rarely used in studying the detection and distribution of jellyfish in marine ecosystem. To investigate the technique’s applicability in detecting and monitoring marine gelatinous zooplankton, eDNA was used to monitory the compass jellyfish (Chrysaora hysoscella) in the southern North Sea. eDNA samples were collected from the surface water of the nine studied stations in the Belgian part of the North Sea (BPNS) from 2014 to 2016. In this study, eDNA samples from October 2014, March, May, August and October 2015, January, March, May and August 2016 were extracted using CTAB. eDNA extracts were run in a qPCR for C. hysoscella eDNA detection and quantification.This study detected C. hysoscella eDNA in the BPNS across the sampling months with a reduction in the frequency of detection in 2016. The target eDNA was found to be more common in Oostende then in Nieuwpoort and least in Zeebrugge stations. C. hysoscella eDNA was common and abundant in offshore stations and least in the shoreline stations. Peaks of eDNA abundance were recorded in spring, summer and autumn periods (October 2014, March, May and August 2016, March and August 2016). The recorded eDNA abundance was found to be not correlated with temperature (p = 0.4254). The results also revealed that the abundance of C. hysoscella eDNA somehow exhibited temporal and spatial variations. The results of this study imply that eDNA approach can be used to study the presence, patterns of distribution and the estimates of C. hysoscella biomass in the BPNS. This study confirms the broad potential of eDNA method in surveying ecosystems. The eDNA protocol used in the present study can be developed further to monitor jellyfish population in the BPNS obtaining a more detailed estimates of jellyfish abundance and distribution.