Animal vocalisations play a role in individual recognition and mate choice. In nesting penguins, acoustic variation in vocalisations originates from distinctiveness in the morphology of the vocal apparatus. Using the source-filter theory approach, we investigated vocal individuality cues and correlates of body size and mass in the ecstatic display songs the Humboldt and Magellanic penguins. We demonstrate that both fundamental frequency (f0) and formants (F1-F4) are essential vocal features to discriminate among individuals. However, we show that only duration and f0 are honest indicators of the body size and mass, respectively. We did not find any effect of body dimension on formants, formant dispersion nor estimated vocal tract length of the emitters. Overall, our findings provide the first evidence that the resonant frequencies of the vocal tract do not correlate with body size in penguins. Our results add important information to a growing body of literature on the role of the different vocal parameters in conveying biologically meaningful information in bird vocalisations.