Microorganisms are closely related to skin diseases, and microbiological imbalances or invasions of exogenous pathogens can be a source of various skin diseases. The development and prognosis of such skin diseases are also closely related to the type and composition ratio of microorganisms present. Therefore, through detection of the characteristics and changes in microorganisms, the possibility for diagnosis and prediction of skin diseases can be markedly improved. The abundance of microorganisms and an understanding of the vast amount of biological information associated with these microorganisms has been a formidable task. However, with advances in large-scale sequencing, artificial intelligence (AI)-related machine learning can serve as a means to analyze large-scales of data related to microorganisms along with determinations regarding the type and status of diseases. In this review, we describe some uses of this exciting, new emerging field. In specific, we described the recognition of fungi with convolutional neural networks (CNN), the combined application of microbial genome sequencing and machine learning and applications of AI in the diagnosis of skin diseases as related to the gut-skin axis.