The innate immune system in vertebrates is considered to lack specific memory. To investigate innate immune system based immunological protection mediated by cells that are not part of the acquired immune system the Tübingen recombination activation gene1 (rag1)t26683 mutant (MT) zebrafish was chosen. Molecular analysis demonstrated MT zebrafish kidney cells expressed Non-specific Cytotoxic cell receptor protein-1 (NCCRP-1) and Natural Killer cell (NK) lysin but lacked T cell receptor (TCR) and immunoglobulin (Ig) VH1, VH2, VH3 and VH4 expression. Differential counts of peripheral blood leukocytes indicated that MT fish had decreased lymphocyte populations (34.7%) compared to rag1+/+ wild-type (WT) fish (70.5%), and increased granulocyte populations (34.7%) compared to WT (17.6%). Further, endocytic functions of phagocytes from MT fish were compared to WT fish. No significant differences in the selective and non-selective mechanisms of uptake in phagocytes were observed between MT and WT zebrafish. For the first time it was shown that zebrafish phagocytes utilize macropinocytosis and Ca2+ dependant endocytosis mechanisms for antigen uptake. These characterization studies suggest that MT zebrafish provide a unique model for investigating innate immune responses because fully functional innate defenses are present without the influence of lymphocytes and lymphocyte associated acquired immune responses. To conduct such large scale investigations the first ongoing rag1t26683 mutant zebrafish breeding colony was established. To meet special husbandry needs of immunodeficient MT zebrafish, standard rearing protocols were advanced and the information was made available to the zebrafish community at: http://www.cvm.msstate.edu/zebrafish/index.html. Multiple trials were conducted to evaluate the potential for memory of the innate immune system. Significant reduction in mortality was observed in MT vaccinated zebrafish upon secondary exposure to Edwardsiella ictaluri when compared to unvaccinated, MT fish. This documents for the first time, that MT zebrafish, lacking an acquired immune system, are able to mount a protective immune response to Edwardsiella ictaluri and generate protection upon a repeated encounter to the same pathogen. The observed protection is long lasting and mediated by the innate immune system, but a specific mechanism is not yet defined.