Abstract In zebrafish, the onset of acetylcholinesterase (AChE) expression was detected by RT-PCR at 4 hpf (hours post-fertilization). The aryl acylamidase (AAA) associated with AChE, a serotonin sensitive activity with unknown physiological function, was significantly higher than the esterase activity on zebrafish embryos homogenates at 4–12 h development (test- t = 3.523; d.f. = 4). Remarkably, the ratio of AAA/AChE activity decreased 210-fold from 4 to 144 h development, indicating a distinct embryonic role of AAA during early embryogenesis. The AAA activity was sensitive to eserine and serotonin, ensuring its association with AChE. This is the first report of AAA activity on fish, establishing zebrafish as a model to study AAA on development.