The nodule inception gene Nin is related to early stages of root nodule formation in the model plant Lotus japonicus. Functionally, its homologs, Nin-like genes, are also involved in N metabolism. In this study, Nin-like gene data were retrieved from completely sequencing genomes of legume and non-legume plants for investigating phylogeny to trace the divergence of genes and proteins and build relationships between structural divergence and functional differentiation. We revealed novel Nin-like genes; previously resolved orthologous groups were recovered and their sister relationships resolved. Nin-like genes showed a diversity of structures, which supports the results of phylogenetic and functional studies; OsNLP5 from Oryza sativa was found to be intronless, which probably originated from a gene retroposition event. We found discrepancies in domain organizations and functional sites among NIN-like proteins, which indicates possible functional differentiation. 3-D structural analysis revealed the occurrence of significant conformational changes in GAF domains of NIN-like proteins from nodule legume plants, which could become the basis of recruitment as nodule inception genes. Our findings will contribute to the design of further experimental studies.