Reactive oxygen species (ROS) play important roles during development and responses to external stimuli. In Brassicaceae, the stigma epidermis accumulates a large amount of ROS. Moreover, regulating the stigmatic ROS status is crucial for Self-incompatibility (SI) mechanisms, to ensure self-pollen rejection while promoting compatible pollen. Here, scanning our transcriptomic data in light of recent advances in the Brassicaceae SI system, we identified Class III peroxidases that are highly expressed in mature stigma and might regulate stigma ROS homeostasis. We also found two Receptor Like Kinases from the CYSTEINE-RICH RECEPTOR-LIKE KINASES family (CRK31 and CRK41) strongly upregulated upon incompatible pollination. We proposed that these two CRKs might be part of the ROS-mediated SI response and serve to connect pollen recognition and ROS accumulation.