Some of the most striking behaviors of animals are displays used in courtship, territorial behavior, and in defense against predators. Among reptiles, lizards exhibit enormous diversity in the stereotyped motion patterns of their bobbing displays. Although the bobbing displays of numerous lizard species have been described to date, those of the Galápagos Lava Lizards (Microlophus spp., Tropiduridae) have received comparatively little attention. Here, we analyze bobbing displays from four of the nine lava lizard species: Microlophus albemarlensis, M. bivittatus, M. grayii, and M. indefatigabilis. Field-recorded displays first were standardized to a common amplitude scale, and attributes of display duration and head amplitude were measured. Next, a discrete Fourier transform (DFT) was computed for each display, and data were gathered on 13 frequency and amplitude variables. Then, we conducted a principal components analysis on the Fourier transform–based variables, and used discriminant function analyses (both standard and permuted) to test the strength of species specificity in display structure. Results showed that displays with simpler structure (M. albemarlensis and M. grayii) were more often correctly assigned to species than were displays with more complex structure (M. bivittatus and M. indefatigabilis). We offer predictions for further tests on the bobbing displays of additional species of Galápagos lava lizards, and suggest that DFT represents a promising tool for the analysis of animal motion displays.