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Condition indices correlating body lipid content with mass and morphometric measurements have been developed for a variety of taxa. However, for many large species, the capture and handling of enough animals to obtain representative population estimates is not logistically feasible. The relatively low cost and reduced disturbance effects of UAVs make them ideal for the rapid acquisition of high volume data for monitoring large species. This study examined the imagery collected from two different UAVs, flown at 25 m altitude, and the subsequent georeferenced orthomosaics as a method for measuring length and axillary girth of Australian fur seals (Arctocephalus pusillus doriferus) to derive an index of body condition. Up to 26% of individuals were orientated correctly (prostrate/sternal recumbent) to allow for body measurements. The UAV-obtained images over-estimated axillary girth diameter due to postural sag on the lateral sides of the thorax while the animals are lying flat in the sternal recumbent position on granite rocks. However, the relationship between axillary girth and standard length was similarly positive for the remotely- and physically-obtained measurements. This indicates that residual values from the remotely-obtained measurements can be used as a relative index of body condition.