BackgroundClonostachys roseais an established biocontrol agent. Selected strains have either mycoparasitic activity against known pathogens (e.g.Fusariumspecies) and/or plant growth promoting activity on various crops. Here we report outcomes from a comparative ‘omics analysis leveraging a temporal variation in the in vitro antagonistic activities ofC. roseastrains ACM941 and 88–710, toward understanding the molecular mechanisms underpinning mycoparasitism.ResultsTranscriptomic data highlighted specialized metabolism and membrane transport related genes as being significantly upregulated in ACM941 compared to 88–710 at a time point when the ACM941 strain had higher in vitro antagonistic activity than 88–710. In addition, high molecular weight specialized metabolites were differentially secreted by ACM941, with accumulation patterns of some metabolites matching the growth inhibition differences displayed by the exometabolites of the two strains. In an attempt to identify statistically relevant relationships between upregulated genes and differentially secreted metabolites, transcript and metabolomic abundance data were associated using IntLIM (Integration through Linear Modeling). Of several testable candidate associations, a putativeC. roseaepidithiodiketopiperazine (ETP) gene cluster was identified as a prime candidate based on both co-regulation analysis and transcriptomic-metabolomic data association.ConclusionsAlthough remaining to be validated functionally, these results suggest that a data integration approach may be useful for identification of potential biomarkers underlying functional divergence inC. roseastrains.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09463-6.