In order to propagate reactionary thinking and disrupt social security management, reactionary forces often write and post various reactionary slogans with a marker. Undoubtedly, it’s significant to identify the marker ink in forensic science. The paper collected and analyzed the infrared fingerprint data of 40 black marker pens from 5 brands including Guangbo and so on. Pre-processing used multi-scatter correction, peak area normalization, automatic baseline correction, and Savitzky-Golay smoothing to create a black marker ink identification model based on multilayer perceptron (MLP). The result showed that the infrared fingerprint can reflect the subtle changes of the molecular structure, which can effectively distinguish the water-based and oil-based markers. For 4 oily marker samples, it was found that the MLP model has the best feature extraction on the 30-dimensional matrix, whose accuracy rate reached 100%. Besides, feature 12, feature 26, and feature 17 were of the highest importance in model construction, with 0.0355, 0.0347, and 0.0346, respectively. Among them, the Letu brand samples had a high degree of convergence, concentrated distribution, and the difference in ink composition and content were small, while the Baoke brand samples were the opposite. In the confirmatory analysis, 8 samples to be determined achieved 100% accuracy, which was ideal. In summary, infrared fingerprints combined with multilayer perceptron can achieve accurate identification between black marker ink brands. The method improved the efficiency of inspection and identification, reduced the cost of identification and fulfilled the rapid and accurate inspection goal for frontline law enforcement personnel, which has certain universality and reference significance.