A comparative analysis on protein kinases encoded in the completely sequenced genomes of two plant species, namely Arabidopsis thaliana and Oryza sativa spp japonica cv. Nipponbare is reported in the current study. We have analysed 836 and 1386 kinases identified from A. thaliana and the O. sativa genomes respectively. Their classification into known subfamilies reveals selective expansions of the plant receptor kinase subfamily comprising of Ser/Thr receptor kinases. The presence of calcium dependent kinases, and potential absence of cyclic nucleotide-dependent protein kinase of the type found in other (non-plant) eukaryotes, are other notable features of the two plant kinomes described here. An analysis on domain organisation of each of the protein kinases encoded in the plant genome has been carried out. Uncommon composition of functional domains like nuclear translocation factor domain, redox sensor domain (PAS), ACT and lectin domains are observed in few protein kinases shared between the two plant species. Biochemical functions characteristic of the domains recruited in these protein kinase gene products suggest their mode of regulation by alternate cellular localisation, oxidation potential, amino acid flux and binding of carbohydrates. Occurrence of multi-functional kinases with diverse enzymatic modules, such as Transposases and peptidases, tethered to the kinase catalytic domain is another interesting feature of the protein kinase complement of the O. sativa genome. Co-occurrence of diverse nucleotide and carbohydrate binding domains with catalytic kinase domain containing gene products has also been observed. Putative homologues of protein kinases of A. thaliana that regulate plant-specific physiological processes like ethylene hormone response, somatic embryogenesis and pathogen defence have been identified in O. sativa genome as well.