Infant rodents emit ultrasonic vocalizations when isolated from dam and littermates. Due to the context of their occurrence and the well described bidirectional modulation by substances known for their capability to influence emotionality, it was postulated that such calls reflect a negative affective state akin anxiety. Comparative studies observed pronounced differences in calling behavior between strains, which were paralleled by differences in maternal care. Therefore, it was recently hypothesized that early environmental factors may have strong impact on call production. Here, the relative contributions of genetic background, gender, and early environmental factors on calling behavior in C57BL/6JOlaHsd and C57BL/6NCrl were studied by using an embryo-transfer procedure. The results show that these sub-strains differ in the amount of calling and specific call features, like call frequency and amplitude. The embryo-transfer procedure indicated that the observed differences in the amount of ultrasonic calling are dependent on the dyadic interaction between mother and pup. Conversely, call features were primarily dependent on the genotype of the pup. Thus, call frequency and frequency modulation were solely dependent on the pup, i.e. its genotype and gender. However, there was one exception, namely call amplitude, which was solely dependent on the genotype of the mother, i.e. on early environmental factors. Furthermore, it was shown that particularly changes in call amplitude might be of high functional relevance, since a sub-strain dependent preference towards pups emitting calls with high amplitudes was observed. In total, it can be concluded that both genomic and nongenomic factors can tune calling behavior in mouse pups.