In higher plants, the metabolism of carbon (C) and nitrogen nutrients (N) is mutually regulated and referred to as the C and N balance (C/N). Plants are thus able to optimize their growth depending on their cellular C/N status. Arabidopsis ATL31 and ATL6 encode a RING-type ubiquitin ligases which play a critical role in the C/N status response (Sato et al. in Plant J 60:852-864, 2009). Since many ATL members are involved in the plant defense response, the present study evaluated whether the C/N response regulators ATL31 and ATL6 are involved in defense responses. Our results confirmed that ATL31 and ATL6 expression is up-regulated with the microbe-associated molecular patterns elicitors flg22 and chitin as well as with infections with Pseudomonas syringae pv. tomato DC3000 (Pst. DC3000). Moreover, transgenic plants overexpressing ATL31 and ATL6 displayed increased resistance to Pst. DC3000. In accordance with these data, loss of ATL31 and ATL6 function in an atl31 atl6 double knockout mutant resulted in reduced resistance to Pst. DC3000. In addition, the molecular cross-talk between C/N and the defense response was investigated by mining public databases. The analysis identified the transcription factors MYB51 and WRKY33, which are involved in the defense response, and their transcripts levels correlate closely with ATL31 and ATL6. Further study demonstrated that the expression of ATL31, ATL6 and defense marker genes including MYB51 and WRKY33 were regulated by C/N conditions. Taken together, these results indicate that ATL31 and ATL6 function as key components of both C/N regulation and the defense response in Arabidopsis.