Despite the key function of the Mauthner cells (M-cells) in initiating escape responses and thereby promoting survival, there are multiple examples of M-cell loss across the teleost phylogeny. Only a few studies have directly considered the behavioral consequences of naturally occurring M-cell variation across species. We chose to examine this issue in pufferfishes, as previous research suggested that there might be variability in M-cell anatomy in this group of fish. We characterized the M-cell anatomy and fast-start responses of two pufferfish species, Tetraodon nigroviridis and Diodon holocanthus. T. nigroviridis showed robust fast-starts to both tactile and acoustic startling stimuli. These fast-starts occurred with a latency typical of M-cell initiation in other fish, and retrograde labeling of spinal-projection neurons revealed that T. nigroviridis does have M-cells. By contrast, D. holocanthus only rarely exhibited fast-start-like behavior, and these responses were at a substantially longer latency and were much less extensive than those of T. nigroviridis. Using three complementary anatomical techniques we were unable to identify obvious M-cell candidates in D. holocanthus. These results provide a clear correlation between M-cell presence or absence and dramatic differences in fast-start behavior. The rich diversity within the pufferfish clade should allow future studies investigating the factors that contribute to this correlated anatomical and behavioral variation.