From the sequences of Rel/NF-kB and IkB proteins, we constructed an alignment of their Rel Homology Domain (RHD) and ankyrin repeat domain. Using this alignment, we performed tree reconstruction with both distance matrix and parsimony analysis and estimated the branching robustness using bootstrap resampling methods. We deÂźned four subfamilies of Rel/NF-kB transcription factors: (i) cRel, RelA, RelB, Dorsal and Dif; (ii) NF-kB1 and NF-kB2; (iii) Relish and (iv) NF-AT factors, the most divergent members. Subfamilies I and II are clustered together whereas Relish diverged earlier than other Rel/NF-kB proteins. Three subfamilies of IkB inhibitors were also deÂźned: (i) NF-kB1 and NFkB2; (ii) close to subfamily I, the short IkB proteins IkBa, IkBb and Bcl-3; (iii) Relish that diverged earlier than other IkB inhibitors. Our deÂźnition of groups and subfamilies Âźts to structural and functional features of the Rel/NF-kB and IkB proteins. We also showed that ankyrin repeats of NF-kB1, NF-kB2 and Relish are short IkB-speciÂźc ankyrin motifs. These proteins deÂźning a link between Rel/NF-kB and IkB families, we propose that all these factors evolved from a common ancestral RHD-ankyrin structure within a unique superfamily, explaining the speciÂźcities of interaction between the di erent Rel/NF-kB dimers and the various IkB inhibitors.