Being an effective biocontrol agent,Clonostachys rosea possess morphologically two different kinds of conidiophore structures, verticillate and penicillate respectively. However, the factors that influenced this morphological pleomorphism and its related genetic background remains to be elucidated. In this study, single-spore isolates were obtained from these two types of conidiophores and observed for their cultural and morphological characteristics. The stability of pleomorphism was confirmed through three-months of continuous inoculation and incubation. Additionally, the influences on conidiophore’s morphology under different cultural conditions were also recorded. Our data indicated that the fungal inhibitor thiabendazole changed the formation of conidiophores with only verticillate type produced, which subsequently had effects on its abilities to infect the plant pathogenic fungusRhizoctonia solani and nematodesPanagrellus redivivus in our bioassay. However, the genomic analysis by Random Amplified Polymorphic DNA (RAPD) assay showed no obvious differences detected in the mutant with only verticillate conidiophores and its parent strain, suggesting the change in conidiophore’s type should be attributed to different transcriptional patterns.