Melatonin and the plant hormone auxin (indole-3-acetic acid) have some structural similarity and, may thus exert comparable physiological effects on reproduction and growth. To test this possibility, I examined the effects of melatonin and auxin administration on reproductive and non-reproductive organ development in an animal model, the marsh rice rat Oryzomys palustris. Juvenile males housed under 14L:10D conditions were injected daily for four weeks with saline, melatonin, auxin, or melatonin and auxin, and the development of the testes and other organs was assessed. Melatonin alone significantly inhibited the development of the testes, seminal vesicles, Harderian glands, and overall somatic growth, but not the spleen. Auxin did not affect any endpoint measured. When melatonin was administered simultaneously with auxin, the melatonin effects dominated in suppressing reproduction and growth. The administration of melatonin or auxin in the drinking water produced results similar to the effects of melatonin and auxin injections reported herein. Lastly, both melatonin and auxin in the drinking water failed to alter any short photoperiod-induced reproductive inhibition. These data suggest that structural similarities between melatonin and auxin do not result in similar postnatal effects on reproductive and non-reproductive organ development on a long photoperiod and further suggest that melatonin and auxin do not operate through a common physiological mechanism.