The plant hormone, indoleacetic acid (IAA), transcriptionally activates two early genes in pea, PS-IAA4/5 and PS-IAA6 that encode short-lived nuclear proteins. The identification of the nuclear localization signals (NLS) in PS-IAA4 and PS-IAA6 using progressive deletion analysis and site-directed mutagenesis is reported. A C-terminal SV40-type NLS is sufficient to direct the beta-glucuronidase reporter to the nucleus of transiently transformed tobacco protoplasts, but is dispensible for nuclear localization of both proteins. The dominant and essential NLS in PS-IAA4 and PS-IAA6 overlap with a bipartite basic motif which is polymorphic and conserved in related proteins from other plant species, having the consensus sequence (KKNEK)KR-X(24-71)-(RSXRK)/(RK/RK). Both basic elements of this motif in PS-IAA4, (KR-X41-RSYRK), function interdependently as a bipartite NLS. However, in PS-IAA6 (KKNEKKR-X36-RKK) the upstream element of the corresponding motif contains additional basic residues which allow its autonomous function as an SV40-type monopartite NLS. The spacer-length polymorphism, X(24-70), in respective bipartite NLS peptides of several PS-IAA4-like proteins from Arabidopsis thaliana does not affect nuclear targeting function. The structural and functional variation of the bipartite basic motif in PS-IAA4-like proteins supports the proposed integrated consensus of NLS.