Allopolyploidy is a major mode of speciation in flowering plants and particularly in the grass tribe Andropogoneae, which includes sugarcane (Saccharum officinarum) and relatives. A new species of Saccharum from South America (S. intermedium) is described here, supported by morphological, molecular and cytogenetic evidence. Previous molecular analyses indicated an allopolyploid origin of the new species through interspecific hybridization between S. angustifolium and S. villosum. The new taxon has intermediate morphology between the two parental species. Cytogenetic analyses of the three species were performed, including chromosome counts, meiotic regularity, and pollen viability and morphology. The new taxon is hexaploid (2n = 60), while the parental species are triploids (2n = 30), confirming the ploidy level suggested by the number of paralogues in phylogenetic trees based on low-copy nuclear genes. This represents the first chromosome count for S. intermedium and a new cytotype for S. villosum. Although both parental species are triploids, they surprisingly exhibited regular meiosis and high pollen viability, indicating they are male-fertile, as is the hexaploid new species. Data on geographic distribution and phenology is also presented, aswell as a key for the South American species of Saccharum.