Semaphorins are a large family of guidance molecules identified by an extracellular SEMA domain. Classes 1 and 2 are derived from invertebrates, classes 3–7 are vertebrate and class 8 (v) are viral semaphorins. Class 6 semaphorins are reported to have a wide variety of roles including in axon guidance, transcriptional regulation and cancer. Here we report the identification and expression of four class 6 semaphorins (6A, 6Ba, 6Bb and 6Dl) in three stages of larval development in zebrafish (24, 48 and 72 hours postfertilization). Our data indicate that each of the class 6 semaphorins shows a distinct pattern of expression in the developing nervous system that is dynamic over the first 3 days of embryonic development. These data suggest that the individual class 6 semaphorins have diverse roles in nervous system development.