Forensic laboratories are often faced with cases in which methamphetamine hydrochloride-mixed blood is unable to be identified as human blood by immunochromatography against human hemoglobin A0. The application of mRNA expression analysis to samples that showed a false-negative with immunochromatography was investigated as an alternative approach that did not depend on the antigen-antibody reaction. Real-time PCR was used to examine the expression levels of blood markers such as glycophorin A, spectrin beta, and hemoglobin beta. Hemoglobin beta was the only marker that was specifically detected in blood, while glycophorin A was useful for determining human specificity. Hemoglobin beta showed good detection sensitivity and was detectable in 37-year-old blood stains. Hemoglobin beta was exclusively detectable in methamphetamine hydrochloride-mixed blood stains. Detergents and disinfectants did not significantly influence mRNA markers. The proposed mRNA expression analysis was suitable for human blood identification as an alternative method to immunochromatography.