A total of 106 maize seed samples were collected from different agro-climatic regions of
India. Sixty-two Fusarium isolates were recovered, 90% of which were identified as Fusarium verticillioides
based on morphological and molecular characters. Use of the tef-1alpha gene corrected/refined
the morphological species identifications of 11 isolates, and confirmed those of the remaining isolates. Genetic diversity
among the Fusarium isolates involved multilocus fingerprinting profiles by Inter Simple Sequence Repeats (ISSR) UPGMA
and tef-1 alpha gene phenetic analyses; for which, we observed no significant differences among the isolates based on
geographic origin or fumonisin production; most of the subdivision related to species. Genotyping was performed on the
F. verticillioides isolates, using 12 primer sets from the fumonisin pathway, to elucidate the molecular basis of fumonisin
production or non-production. One fumonisin-negative isolate, UOMMF-16, was unable to amplify nine of the 12 fumonisin
cluster genes tested. We also used the CD-ELISA method to confirm fumonisin production for our 62 Fusarium
isolates. Only 15 isolates were found to be fumonisin-negative. Interestingly, genotypic characterization revealed six isolates
with various gene deletion patterns that also tested positive for the production of fumonisins via CD-ELISA. Our
findings confirm the importance of molecular studies for species delimitation, and for observing genetic and phenotypic
diversity, among the Fusaria.