Stable carbon (δ13C) and nitrogen (δ15N) isotopes are used frequently to describe the trophic ecology of top marine mammal predators. Australian sea lions (Neophoca cinerea) are one of the world's rarest otariid seals and exhibit the highest levels of natal site philopatry of any seal. We report the development of a screening technique to identify different foraging ecotypes and assess their relative frequencies in Australian sea lion breeding colonies using stable isotope ratios in pups. Geospatial and dive data from 15 adult females at three breeding colonies revealed alternate foraging strategies (inshore and offshore foraging) that were reflected in significant changes in δ13C and δ15N. Isotope fractionation from mother to pup was validated using paired whisker and blood serum samples with no significant difference between δ13C and δ15N enrichment of +1.27‰ (whiskers) and +1.92‰ (blood serum) from mothers to pups. Isotope ratios from whisker samples representing over 50% of pups born at three colonies revealed significant intercolony differences in maternal foraging ecotype frequencies. These results are unique in that ecological partitioning over such a small spatial scale has not been described in any other otariid species.