Intraspecific variation in acoustic signals may reflect local variation in the intensity of natural and sexual selection and random drift. We examined intraspecific variation in the advertisement call of Spicospina flammocaerulea, a southwestern Australian frog species with a limited distribution, fragmented range, small population sizes, and specific breeding habitat requirements. Of the six populations examined, one in particular differed significantly in dominant frequency and body size. There was no relationship between among-population geographic distance and among-population divergence in call structure suggesting that the divergence is not caused by random drift. A correlation analysis detected a positive relationship between the size of males and females found in amplexus. However, there was no evidence of mated males differing in size from unmated males indicating that the differences in dominant frequency are unrelated sexual selection. Call structure variation may reflect differences in recruitment and resultant age structure of local populations.