Mutations in the dysferlin gene give rise to limb-girdle muscular dystrophy R2, commonly known as dysferlinopathy. This condition is characterized by a late-onset, progressive muscle weakness that initially manifests in the hip and shoulder muscles during young adulthood, and subsequently worsens over time. Our prior research identified a strong correlation between adipogenic muscle replacement and the progression of dysferlinopathy. Preclinical interventions that halted this process effectively prevented the advancement of muscle loss, pinpointing intramuscular adipogenesis and the interactions of stromal cells as the disease mechanism in dysferlinopathy. To identify the aberrant stromal cell populations and their underlying dysregulation, we conducted a comprehensive single-cell RNA-Seq analysis on stromal cells from both affected and unaffected muscles in a dysferlin-deficient mouse model. We examined them along disease progression from asymptomatic (4 months) to late symptomatic (11 months) ages. This yielded transcriptomic data from ~170,000 stromal cells from dysferlin-deficient and matched healthy muscles, and identified the chronic emergence of novel macrophage and fibro/adipogenic progenitor (FAP) sub-populations as the principal contributors to the onset and progression of dysferlinopathy. Interactome analysis of these pathogenic cell subpopulations identified aberrant intercellular signaling linked to the adipogenic transformation of FAPs and the transition of muscle tissue into a symptomatic state. We confirmed these findings through microscopic analysis by correlating the accumulation of these pathogenic macrophage and FAP subpopulations as well as revealing their close spatial association within the muscle tissue in vivo, which is linked to muscle pathology. Through in vitro experiments involving the co-culture of these isolated pathogenic subpopulations, we confirmed that disease-enriched macrophages promote FAP adipogenesis. We will present this data and our results of modifying these interactions as a potential mechanism for progressive fatty replacement and its inhibition in dysferlinopathy, opening targeted avenues to leverage these findings into effective therapy for these patients.