The IKK-NF-κB signaling cascade is one of the crucial responsive mechanisms in inflammatory and immune responses. The key kinase proteins called inhibitor of kappa B kinases (IKKs) serve as the core elements involved in cascade activation. Here, the complete ORFs of IKK homologs,
PmIKK
β
,
PmIKK
ε
1
, and
PmIKK
ε
2
, from the black tiger shrimp
Penaeus monodon
were identified and characterized for their functions in shrimp antiviral responses. The
PmIKK
transcripts were widely expressed in various examined tissues and the
Pm
IKKε protein was detected in all three types of shrimp hemocytes. Only the
PmIKK
ε
1
and
PmIKK
ε
2
were responsive to white spot syndrome virus (WSSV), yellow head virus (YHV) and a bacterium
Vibrio harveyi
infection, while the
PmIKK
β
exhibited no significant response to pathogen infection. On the contrary, suppression of
PmIKK
β
and
PmIKK
ε
by dsRNA-mediated RNA interference (RNAi) resulted in a rapid death of WSSV-infected shrimp and the significant reduction of an IFN-like
PmVago4
transcript. Whereas, the mRNA levels of the antimicrobial peptides,
ALFPm3
and
CrustinPm5
, and a transcription factor,
PmDorsal
were significantly increased, those of
ALFPm6, CrustinPm1, CrustinPm7, PmVago1, PmRelish
, and
PmCactus
were unaffected. Overexpression of
Pm
IKKβ and
Pm
IKKε in HEK293T cells differentially activated the NF-κB and IFNβ promoter activities, respectively. These results suggest that the
Pm
IKKβ and
Pm
IKKε may act as common factors regulating the expression of immune-related genes from various signaling pathways. Interestingly, the
Pm
IKKs may also contribute a possible role in shrimp cytokine-like system and cross-talking between signaling transductions in innate immune responses.