Population variation in primate vocal structure has been rarely observed. Here, we report significant population differences in the structure of two vocalizations in wild pygmy marmosets (Trills and J calls). We studied 14 groups of pygmy marmosets Callithrix (Cebuella) pygmaea pygmaea from five populations in northeastern Ecuador. We analyzed the acoustic structure of Trills and J calls recorded from two adult animals in each group through focal samples. Although individuals and groups within a population differed in call structure, we found consistent structural differences at a population level for Trills and J calls. Pair-wise comparisons for the two call types point to San Pablo and Amazoonico as the populations that differed the most, whereas Hormiga and Zancudococha showed the least differences. Discriminant function analysis indicates that calls from each population could be classified accurately at rates significantly above chance. Habitat acoustics, social factors and genetic drift may explain interpopulation vocal differences. This is the first evidence of within-subspecies vocal differences, or dialects, in wild populations of a neotropical primate species. Am. J. Primatol. 71:333-342, 2009.