A negative relationship between cetacean body size and tonal sound minimum and maximum frequencies has been demonstrated in several studies using standard statistical approaches where species are considered independent data points. Such studies, however, fail to account for known dependencies among related species—shared similarity due to common ancestry. Here we test these hypotheses by generating the most complete species level cetacean phylogeny to date, which we then use to reconstruct the evolutionary history of body size and standard tonal sounds parameters (minimum, maximum, and center frequency). Our results show that when phylogenetic relationships are considered the correlation between body size (length or mass) and minimum frequency is corroborated with approximately 27% of the variation in tonal sound frequency being explained by body size compared to 86% to 93% explained when phylogenetic relationships are not considered. Central frequency also correlates with body size in toothed whales, but for other tonal sound frequency parameters, including maximum frequency, this hypothesized correlation disappears. Therefore, constraints imposed by body size seem to have played a role in the evolution of minimum frequency but alternative hypotheses are required to explain variation in maximum frequency.