In Brassicaceae self‐incompatibility (SI), self‐pollen rejection is initiated by the S‐haplotype specific interactions between the pollen S cysteine‐rich/S‐locus protein 11 (SCR/SP11) ligands and the stigma S receptor kinases (SRK). In Brassica SI, a member of the Plant U‐Box (PUB) E3 ubiquitin ligases, ARM‐repeat containing 1 (ARC1), is then activated by SRK in this stigma and cellular events downstream of this cause SI pollen rejection by inhibiting pollen hydration and pollen tube growth. During the transition to selfing, Arabidopsis thaliana lost the SI components, SCR, SRK, and ARC1. However, this trait can be reintroduced into A. thaliana by adding back functional copies of these genes from closely related SI species. Both SCR and SRK are required for this, though the degree of SI pollen rejection varies between A. thaliana accessions, and ARC1 is not always needed to produce a strong SI response. For the A. thaliana C24 accession, only transforming with Arabidopsis lyrata SCR and SRK confers a strong SI trait (SI‐C24), and so here, we investigated if ARC1‐related PUBs were involved in the SI pathway in the transgenic A. thaliana SI‐C24 line. Two close ARC1 homologs, PUB17 and PUB16, were selected, and (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) technology was used to generate pub17 and pub16 mutations in the C24 accession. These mutants were then crossed into the transgenic A. thaliana SI‐C24 line and their potential impact on SI pollen rejection was investigated. Overall, we did not observe any significant differences in SI responses to implicate PUB17 and PUB16 functioning in the transgenic A. thaliana SI‐C24 stigma to reject SI pollen.