In studies of the function of neurofilaments in the squid giant axon we showed that isolated neurofilament preparations from axoplasm are associated with high levels of casein kinase-like activity. To determine the role of these kinases in phosphorylation of neurofilament proteins, we isolated two kinases from squid brain which are also found in axoplasm, CK I and CK II. The CKI is similar to this axonal neurofilament-associated CKI-like kinase activity. CK I displayed a high specificity for the squid high molecular weight (NF220) and rat high molecular weight (NF-H) neurofilament proteins relative to alpha-casein, phosvitin, and middle (NF-M) and low (NF-L) rat neurofilament proteins. The brain CKII, with activity similar to that found in axoplasm, but not associated with neurofilaments, poorly phosphorylated NF220 and NF-H, while demonstrating similar affinities, relative to CK I, for NF-M, NF-L, alpha-casein, and phosvitin. The high affinity of squid neuronal CKI for squid NF220 and rat NF-H and its association with axonal neurofilaments suggest that this kinase may have a specific role in neurofilament phosphorylation essential for interaction with other cytoskeletal elements in the axon.