Schizothorax macropogon is one of the main economic fishes in Tibet area, only distributed in the upper and middle reaches of the Yarlung Tsangpo River and its tributaries. Saprolegniasis is one of the most difficult fish diseases in prevention and control, and brings huge economic losses to the aquaculture industry. This experiment was conducted to analyze the effects of Saprolegniasis on the spleen transcriptome of S. macropogon and understand the molecular mechanisms of S. macropogon infected by Saprolegniasis. A total of 5 healthy and 5 Saprolegnia infected S. macropogon living in the same aquatorium were randomly selected. The PDA agar medium and molecular biology methods were used for isolation and identification the S. strain from S. Macropogon. In addition to the transcriptomes of spleen tissues of healthy and fungus infection, S. macropogon were sequenced based on the Illumina HiSeq^TM 2000 high-throughput sequencing platform and the data were analyzed by bioinformatics tools in this study. The research showed that we obtained 3 S. strains from the skin of S. Macropogon, including S. parasitica and S. ferax. A total of 46 619 504 and 43 912 876 clean reads were obtained in the healthy group and fungus infection group, respectively. 359 164 transcripts were assembled and 123 863 unigenes were spliced after removing redundancy. Compared with the healthy group, 1 889 unigenes showed differential expressions in the fungus infection group, 1 414 unigenes were up-regulated and 475 unigenes were down-regulated among these genes. Six differentially expressed unigenes (natural killer cells-lysin gene, somatostatin gene, preproinsulin gene, chymotrypsin gene, protein disulfide isomerase gene and prolactin receptor gene) were randomly selected for quantitative real-time PCR and the results were consistent with the RNA-seq. The results of GO functional enrichment showed that the up-regulated genes are mainly enriched in 241 terms, and down-regulated genes are mainly enriched in 60 terms. These genes involve molecular functions, cell components and biological processes. Besides, among these GO functions, the most differentially expressed genes were enrichment in biological processes, including muscle contraction, muscle system process and muscle structure development. KEGG pathway enrichment suggested that the unigenes were enriched in immune diseases, endocrine and metabolic diseases, viral infectious diseases, digestive system, excretory system and so on. Collectively, the results of above indicate that infection with Saprolegnia can affect genes expression in the spleen tissue of S. macropogon. The conclusion will provide important references for further exploration of the S. infection mechanism of S. macropogon.