[Objectives] Single-cell RNA sequencing was used to investigate the cellular composition of the three hematopoietic organs-kidney, liver, and spleen of Gymnocypris eckloni. The study aims to systematically map the cellular composition of these organs, and to accumulate scientific data for the study of the haematopoietic system, particularly erythropoiesis, in this species. [Methods] Single-cell suspensions were prepared and sequenced using single cell RNA sequencing software to clarify the characteristics and differences in the distribution of cells in the haematopoietic organs and to construct a preliminary cellular atlas of the haematopoietic organs of G. eckloni. [Results] Cells within the three organs of G. eckloni were initially classified into 16 subpopulations based on the sequencing results (Fig. 2). This, combined with the expression of the top 20 differentially expressed genes and known marker genes for each cell population, identified a variety of cell types. These included erythrocytes, neutrophils, T cells, B cells, dendritic cells, epithelial cells, macrophages, vascular endothelial cells, myoblasts, fibroblasts, monocytes and neuronal cells. There is considerable heterogeneity in the distribution of cells in the three organs (Fig. 4). The G. eckloni had a relatively large distribution of cell populations involved in erythrocyte functions, the kidney had a relatively large distribution of cell populations involved in the immune response, and the liver had a relatively large distribution of vascular endothelial cells and myocytes. [Conclusion] The similarity to the haematopoietic cell types of the Zebrafish Danio rerio demonstrates the high conservation of haematopoietic cell development and evolution. According to functional enrichment analysis, G. eckloni, like most scleractinian fishes, has kidneys, spleen and liver, which are not only involved in haematopoiesis and erythropoiesis, but also play roles in immune system development, response and other processes. Meanwhile, the present study complements and improves the study of the haematopoietic phylogeny of G. eckloni from a single-cell perspective, shows the characteristics and differences of cell distribution in different haematopoietic tissues, and provides a certain research basis for further predicting the developmental path of erythrocytes in G. eckloni.