Fish otolith chemistries are used to associate fishes with specific environments. However, otolith chemistry may also have potential as a tool in phylogenetic research, as demonstrated here in salmoniform fishes and related taxa. Two-dimensional maps of Zn:Ca otolith chemistry displayed annual oscillations in magnitude in members of the Salmoniformes (with salmons differing from whitefishes). These are also detectable in esocids, but not strongly in osmerids or in more distantly related taxa. Further, Zn:Ca magnitudes were highest in salmonids and declined in other taxa: salmonids (salmons, grayling, and whitefishes) > esocids > osmerids > other. We performed spatial analysis on sagittal section Zn:Ca maps, dividing them into five zones and obtaining means within each zone, as well as grand means. Discriminant function analysis of the different otolith zones was better able to separate taxonomic groups, but showed pike grouping more closely with salmonids and osmerids with the out-group. Zn:Ca incorporation in otoliths may be a trait under phylogenetic control, and recent re-ordering of the systematics of Salmoniformes and their sister groups may be supported by otolith Zn:Ca chemistry.