Most heterosis research has been focused on growth vigor or increased yield and there is little research on heterosis and stress tolerance. The yield traits of plants depend of the male reproductive development including microsporogenesis and microgametogenesis, that is extremely sensitive to adverse climatic environments and abiotic stresses typically resulting in male sterility. The transcriptomic studies often suggest a complex genetic architecture underlying heterosis, being documented non-additive gene expression patterns in hybrids. Thus, transcripts analysis by RT-qPCR was employed to identify the differences in expression profiles of some meiosis and microsporogenesis related genes in sunflower F1 hybrid relative to its parents, thus underlying heterotic responses. The florets from inflorescence buds (R1-R3) were subjected to microscopical, physiological and molecular analyses. The model of additive/nonadditive genes expression was used to compare transcripts profiles between F1 hybrid and its parents. All studied sunflower transcripts (associated with mitochondrial stability, DNA repair and recombination) are differentially expressed. Also, the transcriptomic data showed more non-additive gene expression patterns in hybrids than additive revealing, often, microsporogenesis stage specificity. It is suggested that the genes with expression changes in F1 hybrids (non-additively) can be associated with heterosis and those involved in specific signaling pathways could be targeted regulated.