The BIRD protein JACKDAW (JKD) belong to the INDETERMINATE DOMAIN (IDD) protein family shown to regulate many developmental processes in plants. JKD encodes a Zinc Finger Protein expressed in the root ground tissue and regulates root patterning in Arabidopsis thaliana (Arabidopsis). Recent and unpublished study indicates that JKD is involved in plant defense response in Arabidopsis. Here we study the JKD function in tomato plants (Solanum lycopersicum). We analyzed the tomato JKD orthologues (Solyc09g007550 (Solyc09) and Solyc10g084180 (Solyc10)) mutant lines, which were generated by Crispr-Cas and TILLING (Targeting Induced Local Lesions in Genomes). Our data indicate that, like in Arabidopsis, Solyc09 controls root ground tissue patterning; the mutant lines show extra cell division in the inner cortex and disturbed stem cell patterning. In addition, we found that both Solyc09 and Solyc10 control the root and stem thickness and regulate tomato leaf shape. To further investigate whether Solyc09 and Solyc10 have a function in tomato when subjected to biotic stress, we evaluated the mutants response to the necrotrophic fungi Botrytis cinerea. We found that the tomato bird mutants have less infection when compared to the control. Taken together our data show that Solyc09 and Solyc10 genes play an essential role in tomato root, shoot development, and in plant immune response to the pathogenic fungi.