Predator-prey interactions based on laterality have recently been observed between fishes and their prey populations. Maintenance of antisymmetric dimorphism by frequency-dependent selection has been reported in fish, but has not been observed in invertebrates. Over 10 years, we investigated long-term changes in the “ratio of laterality” (frequency of righty morphs in a population) in the cuttlefish Sepia recurvirostra and its potential prey prawns Penaeus semisulcatus and Metapenaeus endeavouri in the Visayan Sea, the Philippines. The morphological laterality of cuttlefish and prey prawns was defined by measuring the asymmetry of the cuttlebone and carapace, respectively. Cuttlefish and prey prawns showed morphological antisymmetry, being composed with righty morphs and lefty morphs. The ratio of laterality of cuttlefish and one prey prawn oscillated significantly, but the oscillation was not strongly synchronized. The ratio of laterality of cuttlefish followed that of the prey prawn, indicating that predation biased to each laterality occurred in relation to their laterality. These results suggest that the lateral dimorphism of cuttlefish is maintained through frequency-dependent selection on lateral morphs of the predator cuttlefish and prey prawns. Our findings provide new insight into the ecological significance and antisymmetry maintenance mechanism in relation to interspecific interactions in marine invertebrates.