Chironex fleckeri is considered the most dangerous cubozoan species and poses a considerable risk to both human health and enterprise. Despite this, considerable knowledge gaps surrounding the ecology of C.fleckeri exist. These gaps are largely due to the challenges associated with detection of cryptic life-stages and adults. Environmental DNA has the potential to overcome these detection challenges by providing a means to detect the species at any life-stage in a locality without need of morphological identification. Here we developed a TaqMan-based assay, multiplexed with an endogenous control, and investigated the techniques’ ability to detect C.fleckeri. We first examined C.fleckeri’s eDNA ecology by determining its decay rate and explored if temperature influenced this rate. We then applied the technique in-situ to compare distributions of medusae collected in nets with detection results from eDNA sampling. Both techniques showed similar spatial patterns yet eDNA displayed a greater detection ability. From this, we identified jellyfish hotspots and it is hypothesised that densities of polyps will be greatest at these locations. eDNA sampling was undertaken in winter, when medusae were absent, to explore this hypothesis and examine eDNA's ability to detect cryptic life-history stages. eDNA has potential to advance our current knowledge surrounding cubozoan ecology.