In the present investigation, prevalence, genetic diversity, and mycotoxin producing potential of
Fusarium
species associated with maize grain samples were studied from different geographical regions of India. The highest prevalence of
Fusarium verticillioides
was recorded as 88.52%, followed by
F
.
coffeatum
,
F
.
foetens
, and
F
.
euwallaceae,
6.55%, 3.27%, and 1.63%, respectively. We isolated 54 strains of
F
.
verticillioides
, and their genetic diversity was studied by inter simple sequence repeats (ISSR). The ISSR fingerprints (AG) 8C and (AG) 8G showed 252 and 368 microsatellite sites in the genome of
F
.
verticillioides
and resulted in 99-100% repeatability and reproducibility. The Simpson (SID) and Shannon (H) indices (0.78 and 2.36) suggest that
F
.
verticillioides
strains exhibit moderate to high diversity. Molecular detection of fumonisin B1 (FB1) biosynthetic genes (
FUM1
and
FUM13
) involved in FB1 production in
F
.
verticillioides
was confirmed by polymerase chain reaction (PCR). Furthermore, 91% of the strains were positive for FB1 production, which was affirmed by liquid chromatography with tandem mass spectrometry (LC-MS-MS).
In-vitro
appurtenance of
F
.
verticillioides
spores exhibited a high to moderate effect on the growth and development of the maize. The current finding demonstrated that most
F
.
verticillioides
strains showed a wide range of genetic diversity with varied toxigenic and pathogenic potentials. In conclusion, for the first time,
F
.
coffeatum
,
F
.
foetens
, and
F
.
euwallaceae
species were reported from maize grain samples in India. They were positive for FB1 and negatively affecting grain quality, which is a major concern in food safety.