The invention provides a gene chip and a kit for detecting invasive fungal pathogenic bacteria. The gene chip comprises a solid phase vector and an oligonucleotide probe fixed on the solid phase vector, wherein the probe contains DNA (Deoxyribose Nucleic Acid) sequences selected from 18S to 5.8S or 5.8S to 28S inside transcription regions (ITS) of rDNA and 5.8S rDNA of candida albicans, candida parapsilosis, candida tropicalis, candida kefyr, candida drusei, candida lusitaniae, candida glabrata, candida guilliermondii and cryptococcus neoformans as well as 5.8S rDNA of the nine fungus. The gene chip and the kit of the invention are utilized to detect nine kinds of common pathogenic bacteria, and have the advantages of simple and convenient operation, high accuracy and strong repeatability.