microRNAs regulate dynamic aspects of innate immunity in Arabidopsis thaliana in response to lipopolysaccharides. Lectin-domain receptor-like kinases function as surveillance proteins and miR393 targets transcripts of an L-type LecRK (LECRK-V.7, At3g59740). This study investigated miR393 regulation of LecRLKs associated with LPS perception. Following pre-treatment of wild type -, miR393 ab double mutant - and miR393 overexpressor plants with LPS, the expression of miR393 and two other LecRLK genes (G-type lectin S-receptor-like protein kinases, SD1-13 (At1g11330) and SD1-29 (At1g61380) were evaluated. Overexpression and repression of miR393 respectively suppressed and induced transcripts of the LecRLK genes. The results indicate that miR393 regulates the three LecRLKs following perception of bacterial LPS, in support of immunity and basal resistance. •microRNAs modulate dynamic aspects of innate immunity in Arabidopsis.•miR393 regulates LecRLKs associated with lipopolysaccharide perception.•miR393 targets At3g59740, At1g11330 and At1g61380.•Overexpression of miR393 suppressed transcripts of the LecRLK genes.•Repression of miR393 induced transcripts of the LecRLK genes.