Classically activated macrophages (caMF) play an important role in type-I immune responses and alternatively activated macrophages (aaMF) function in type-II immune responses. While the classical activation of fish macrophages has been well described, the existence of aaMF has not yet been described for teleosts. Arginase is the characteristic enzyme in aaMF and two isoforms have been described for mammals. To study the presence of aaMF in a primitive vertebrate species we cloned arginase 1 and 2 cDNA of common carp. Carp arginase 1 is a 340 aa protein with 63% aa sequence identity to human arginase 1. Carp arginase 2 is a 347 aa protein with 63% aa sequence identity to human arginase 2. Three highly homologous arginase 2 genes were found, each showing only single non-synonymous substitutions. Basal arginase 1 expression is mainly found in carp mid kidney. In contrast, arginase 2 was expressed in all organs examined with the highest basal gene expression in liver. Cultured carp head kidney-derived macrophages were used to study aaMF in vitro. Carp macrophages showed significant arginase activity which could be induced by dibutyryl cyclic adenosine mono phosphate (cAMP) and specifically inhibited by NG-hydroxy-L-arginine (NOHA). At the gene level, arginase 2 gene expression was upregulated by cAMP stimulation, while arginase 1 gene expression was not influenced. LPS stimulation did not alter the arginase 1 or 2 expression, inducible nitric oxide synthase (iNOS) expression was, however, upregulated. This expression of iNOS was used as a measure of classical activation of carp macrophages. Thus, in contrast to mammals, fish arginase 2 and not arginase 1 is differentially regulated and likely involved in the alternative activation of fish macrophages. Our data suggest there may be an evolutionary conservation of the presence of aaMF down to teleost fish.