The p21-activated kinase 1 (PAK1) is a downstream serine/threonine kinase effector of Rac1/Cdc42 that regulates various biological processes including those associating with pathological inflammation. To investigate the function of PAK1 in echinoderms, we isolated a new PAK1 from sea cucumber Apostichopus japonicus ( AjPAK1) by transcriptome database mining and with rapid amplification of cDNA ends (RACE). The full-length cDNA AjPAK1 was 2303 bp in length, containing a 1587 bp ORF encoding 528 amino acid residues. The deduced AjPAK1 contained a p21-Rho-binding domain (PBD) and a serine/threonine protein kinase catalytic domain (S_TKc), which was similar to the PAK1 of crown-of-thorns starfish Acanthaster planci and other eukaryotes. AjPAK1 expressed in all tissues of adult A. japonicus analyzed with the highest transcript anumdance detected in coelomocytes. Significant change in AjPAK1 abundance was observed at 4, 24, 48 and 72 h after Vibrio splendidus infection. Silencing AjPAK1 induced a significant reduction of lysozyme content in coelomic fluid and relative transcript abundances of AjRac1 and AjMKK3/6 in A. japonicus coelomocytes. These results should aid to characterize PAK1 of sea cucumber and decipher its immune function.