MARINE MAMMAL SCIENCE, **(*): ***–*** (*** 2010) C  2010 by the Society for Marine Mammalogy DOI: 10.1111/j.1748-7692.2010.00425.x Detecting alternate foraging ecotypes in Australian sea lion (Neophoca cinerea) colonies using stable isotope analysis ANDREW D. LOWTHER School of Earth and Environmental Science, University of Adelaide, Adelaide, South Australia 5004, Australia and South Australian Research and Development Institute (Aquatic Sciences), P. O. Box 120, Henley Beach, South Australia 5022, Australia E-mail: andrew.lowther@adelaide.edu.au S. D. GOLDSWORTHY South Australian Research and Development Institute (Aquatic Sciences), P. O. Box 120, Henley Beach, South Australia 5022, Australia ABSTRACT Stable carbon ( 13 C) and nitrogen ( 15 N) 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  13 C and  15 N. Isotope fractionation from mother to pup was validated using paired whisker and blood serum samples with no significant difference between  13 C and  15 N 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. Key words: otariid, stable isotopes, foraging ecotypes, foraging behavior, Australian sea lion, sea lion, seal, population structure, whiskers, blood. The use of isotope biochemistry has provided a greater insight into the foraging ecology of a range of mammals (see Crawford et al. 2008 for review). There is strong support for the upward-cascade of stable nitrogen isotopes from primary producers to the top of marine food webs (Hobson et al. 1996). Similarly, trophic level enrichment 1