Schizophrenia patients commonly have sleep disturbances. In this study, we investigated whether single nucleotide polymorphisms (SNPs) in the promoter region of the melatonin receptor genes (MTNR1A and MTNR1B) were associated with schizophrenia and with sleep problems such as insomnia and hypersomnia in schizophrenia patients. We genotyped two promoter SNPs [rs2119882 (-184T/C) of MTNR1A and rs4753426 (-1193C/T) of MTNR1B] using direct sequencing in 289 schizophrenia patients and 505 control subjects. We found that rs2119882 of MTNR1A was associated with schizophrenia in recessive model [CC vs. TT/TC, p = 0.013, odds ratio (OR) = 1.69, 95% confidence interval (CI) = 1.12-2.55]. Interestingly, in an analysis of clinical phenotypes, we found that rs2119882 of MTNR1A was also associated with insomnia symptoms of schizophrenia (recessive model, p = 0.010, OR = 2.24, 95% CI = 1.21-4.14), but not with hypersomnia symptoms as determined using the Operational Criteria checklist. However, rs4753426 of MTNR1B was not associated with either schizophrenia or clinical phenotypes. Our results suggest that MTNR1A may be a susceptibility gene for schizophrenia and may be associated with insomnia symptoms exhibited in schizophrenia patients.