The 29-kDa RNA protein (29RNP), which was originally identified in rice etioplasts, has increased phosphorylation levels during de-etiolation. Here, using heparin-sepharose enriched fractions, we identified a chloroplast kinase that phosphorylated 29RNP. The chloroplast kinase phosphorylated the 29RNP and exhibited CKII biochemical characteristics in a kinase reaction test. Proteomic analysis of the chloroplast heparin-sepharose enriched fractions revealed the presence of 70 proteins, including both abundant proteins, such as plastid encoded polymerase subunits, and low-abundance proteins, such as APO2 and DAG. An inclusion list method using Fourier transform ion cyclotron resonance mass spectrometer ( FT-ICR LTQ MS ) was subsequently used to analyze the chloroplast heparin-sepharose enriched fractions. The 29RNP kinase was positively identified as a CKII alpha family protein by the presence of two unique peptides.