Embryonic ethanol exposure in zebrafish and rats, while stimulating hypothalamic hypocretin/orexin (Hcrt) neurons along with alcohol consumption and related behaviors, increases the chemokine receptor Cxcr4 that promotes neuronal migration and may mediate ethanol's effects on neuronal development. Here we performed a more detailed anatomical analysis in zebrafish of ethanol's effects on the Cxcl12a/Cxcr4b system throughout the entire brain as it relates to Hcrt neurons developing within the anterior hypothalamus (AH) where they are normally located. We found that ethanol increased these Hcrt neurons only in the anterior part of the AH and induced ectopic Hcrt neurons further anterior in the preoptic area, and these effects along with ethanol-induced behaviors were completely blocked by a Cxcr4 antagonist. Analysis of cxcl12a transcripts and internalized Cxcr4b receptors throughout the brain showed they both exhibited natural posterior-to-anterior concentration gradients, with levels lowest in the posterior AH and highest in the anterior telencephalon. While stimulating their density in all areas and maintaining these gradients, ethanol increased chemokine expression only in the more anterior and ectopic Hcrt neurons, effects blocked by the Cxcr4 antagonist. These findings demonstrate how increased chemokine expression acting along natural gradients mediates ethanol-induced anterior migration of ectopic Hcrt neurons and behavioral disturbances.