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<div>Several <i>Fusarium </i>species cause sorghum [<i>Sorghum bicolor </i>(L.) Moench] grain mold, resulting in deterioration and mycotoxin production in the field and during storage. Fungal isolates from air (2005-2006), and from leaves and grain from wild-type and <i>brown midrib </i>(<i>bmr</i>)-<i>6 </i>and <i>12 </i>sorghum plants (2002-2003) at two locations were collected. Plants containing <i>bmr </i>have reduced lignin content, altered cell wall composition and different levels of phenolic intermediates, compared with wild-type. Multilocus maximum likelihood analysis identified two <i>Fusarium thapsinum</i> operational taxonomic units (OTUs). One OTU was identified at greater frequency in grain and leaves of <i>bmr </i>and wild-type plants, but was infrequently detected in air. Nine <i>Fusarium graminearum/Gibberella zeae</i> species complex OTUs were identified: one was detected at low levels in grain and leaves while the rest were only detected in air. Wright’s <i>F-</i>statistic (<i>F_ST</i>) indicated that fungal air populations differentiated between locations during crop anthesis, but did not differ during vegetative growth, grain development and maturity. <i>F_ST</i>also indicated that the <i>Fusarium</i> population from wild-type grain was differentiated from those in either <i>bmr6</i> or <i>bmr12</i> grain at the first location but at the second location, populations from wild-type and <i>bmr6</i> grain were more similar. Thus, impairing monolignol biosynthesis in <i>bmr </i>plants substantially effected <i>Fusarium </i>populations but the environment also had a strong influence.</div>