Background: Sugarcane (Saccharum) is the most important sugar crop in the world. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. Results: A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genome and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which MYB43, MYB53, MYB65, MYB78, and MYB99 were validated by qPCR. Allelic expression dominance in the stem was more significant than that in the leaf, implying the differential expression of alleles may be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. Conclusions: A Genome-wide expression analysis demonstrated that SsMYB genes were involved in stem development and stress response. This study largely contributed to understanding the extent to which MYB transcription factors investigate regulatory mechanisms and functional divergence in sugarcane.