Sugarcane, an important field crop, is cultivated under tropical and subtropical regions around the world. Fusarium sacchari causing wilt, is a stalk disease, inflicting severe damage to the crop in India and other countries. Similarly, pokkah boeng (PB) a foliar disease caused by different species of Fusarium also infects the crop throughout the world. In India, both the diseases occur in different states in various sugarcane varieties. Although both diseases occur independently in the field, we recorded that they occur together in a plant. Hence, a detailed investigation was conducted to characterize different Fusarium isolates from wilt- and PB-affected sugarcane varieties by sequencing TEF1-α gene. Gene sequencing of 48 isolates revealed that 44 were of F. sacchari and the remaining four belonged to F. proliferatum. Of the four F. proliferatum, three were associated with PB and one with wilt. Almost all the 41 wilt-associated isolates belonged to F. sacchari. Investigation carried out to identify Fusarium isolates from the plants exhibiting both the wilt and the PB in two varieties Co 0238 and MS 901 revealed that only F. sacchari caused wilt and PB symptoms in both. Further, several varieties showed progressive disease severity through different phases of PB and that resulted in wilt development. The results clearly established for the first time that the same fungal pathogen systematically infects sugarcane plant and exhibits both the diseases.