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Discoid lateral meniscus (DLM) is more prone to injury than a normally shaped meniscus. No study has compared the gene expression and cell heterogeneity between discoid and normal menisci. We aimed to identify specific cell clusters and their marker genes in discoid meniscus, thereby providing a theoretical basis for the treatment and etiology of DLM. ScRNA-seq was used in DLM and osteoarthritis lateral meniscus (OAM) cells to identify cell subsets and their gene signatures. Pseudo-time analysis and immunohistochemical staining were used to investigate the temporal and spatial distribution of DLM-specific clusters. ScRNA-seq identified nine clusters originating from DLM and OAM, composed of seven empirically defined populations and two novel populations specific to DLM, namely, the prehypertrophic chondrocyte 2 (PreHTC-2) and regulatory chondrocyte (RegC-2) populations. Single-cell trajectory showed that RegC-2 and PreHTC-2 were mainly distributed in a specific cell fate, with the PreHTC-2 marker gene HAPLN1 highly expressed at the end of this fate. Immunohistochemical staining showed that HAPLN1 + cells were mainly distributed in the white zone of DLM.Matrix metalloproteinase (MMP) variants were expressed in DLM and OAM, with MMP2 highly expressed in OAM-dominant cell clusters, while MMP3 was highly expressed in DLM-dominant cell clusters. We concluded that two novel cell clusters including PreHTC-2 were identified using single-cell sequencing, which were mainly distributed in the white areas of DLM. Differentiated MMP expression in the trajectory may be a possible mechanism of DLM formation.