Sterility mosaic disease (SMD) is an emerging biotic risk to the cultivation of pigeonpea throughout the Indian subcontinent. The prevalence and distribution of SMD documented from diverse agro-climatic zones are still poorly known. In this investigation, we determined the spatial distribution of SMD covering major pigeonpea-growing states of Southern India namely, Karnataka, Telangana, Tamil Nadu, Maharashtra, and Andhra Pradesh by considering 2 years of exploratory survey data. Geospatial approaches were employed to determine the SMD incidence levels at unvisited locations using neighboring observations. The results indicated enormous variability in disease incidence ranging from 0 to 82.64% and 0 to 36.84%, respectively, in Kharif 2021–22 and 2022–23 in pigeonpea-growing states. Spatial autocorrelation analysis and Ripley’s K function established the presence of average clustering over sampling locations. Two main clusters were identified via agglomerative hierarchical cluster analysis. From the Local Moran’s I spatial autocorrelation (LISA) analysis, most of the districts were clustered together at (I<0). From the p-values, Bidar and Krishnagiri districts recorded the highest spatial dependence, while the remaining districts recorded medium spatial dependence (p < 0.05). Based on kriging, the Chittoor district of Andhra Pradesh, Medak and Ranga Reddy districts of Telangana, Bijapur district of Karnataka, and Latur district in Maharashtra states were found to be vulnerable to SMD occurrence in the future. The Matern and Spherical models were shown to be the best of the several semivariogram experimental models tested for spatial patterns of SMD incidence, from which OK and IK maps were created. Based on the interpolation results, the potential SMD hotspots/risk areas were most prominent in Telangana, Andhra Pradesh, Karnataka, and Tamil Nadu states. These identified hotspots for SMD revealed high levels of disease probability rates (>25%) above the threshold level and must be closely monitored to restrict and minimize further disease spread across the studied areas in Southern India. In pigeonpea, this is the first study in India that attempted to understand the spatial pattern of SMD using geostatistical methodologies. The results of the study will aid in the design and dissemination of specific management practices and curb the further spread of SMD.