Certain light emitting diodes (LEDs) have become popular in fish farming beacause of a promoting effect on growth and reproduction. However, little information is available on innate immune responses in related tissues under LEDs conditions. The present study assessed the effects of a white fluorescent bulb (the control) and two different light-emitting diodes (LEDs: blue, LDB, peak at 450 nm; red, LDR, 630 nm) on growth and innate immune responses in the serum, liver and ovary of zebrafish for 8 weeks. LDB significantly enhanced specific growth rate (SGR), food intake (FI), and serum globulin levels. In contrast, LDR sharply inhibited SGR, FI, and the levels of albumin and globulin. Under LDB condition, there was an increase in protein levels of alkaline phophatase (AKP) and protein and activity levels of lysozyme (LZM) in the liver, and the levels of mRNA, protein, and activity of LZM in the ovary. Under LDR condition, LZM was dramatically down-regulated at mRNA, protein and activity levels in the ovary, suggesting that LZM was regulated at a transcriptional level. In the liver of the LDR group, though AKP mRNA levels sharply increased, its protein and activity levels significantly declined, indicating that AKP was regulated at translational level. Furthermore, a positive correlation between transcription factor NF-κB RelA mRNA levels and expression levels of AKP and LZM was observed in the liver and ovary, implying a transcriptional regulation of NF-κB RelA. In conclusion, the present study demonstrated a positive effect of LDB and negative effect of LDR on fish growth and innate immune responses, possibly associated with modifications at transcriptional, translational, and post-translational levels, and the transcriptional regulation of the NF-κB signaling molecule.