Chironex fleckeri (box jellyfish) are found in the northern tropical waters of Australia. Although C. fleckeri have a wide geographical distribution and are able to swim large distances, adults tend to stay in small restricted areas. Clinical data shows that deaths from envenoming have not been recorded in Western Australia, yet numerous fatalities have occurred in Northern Territory and Queensland waters. One explanation for this discrepancy is a geographical variation in venom composition. This study examined the pharmacological and biochemical profiles of C. fleckeri venom from different geographical locations and seasons. Venoms were screened for cytotoxicity using a rat aortic smooth muscle cell line (A7r5). While all venoms caused concentration-dependent cytotoxicity, differences were seen in the potency of venoms from Mission Beach and Weipa, when collected in different seasons, as indicated by IC50 values. Similarly venoms collected within the same season, from different locations around Australia, displayed marked differences in venom composition as shown by size exclusion HPLC and SDS-PAGE profiles which indicated the absence or reduced quantity of ‘peaks’ in some venoms. Based on IC50 data obtained from the cell assay, the effects of the most potent (i.e. from Weipa in 2006) and the least potent (i.e. from Broome in 2007) venoms were examined in anesthetised rats. Both venoms at 10 μg/kg (i.v.) caused a transient hypertensive phase followed by cardiovascular collapse. However, at 4 μg/kg (i.v.) venom from Weipa 2006 caused a transient hypertensive phase followed by a transient decrease in MAP while venom from Broome 2007 only caused a small transient increase in MAP. This study demonstrates that there is considerable geographical variation in the composition of C. fleckeri venoms which is most distinct between specimens from western and eastern Australia and may explain the geographical variation in reported deaths.