Proteins have different functions like defense action, structural function, transport action, intracellular signalling etc. As proteins are important in many ways its composition analysis, structure and function determination is required. Protein structure prediction is necessary for drug designing, protein engineering and prediction of binding sites. Phoenix pusilla proteins primary structure prediction was done with Expasy protoparam, secondary structure with SOSUI, tertiary structure with swiss model and transmembrane region was identified with TMHMM v 2.0. Secondary structure prediction of 30SRibosomal protein S3 and RNA polymerase II, showed that α-helix, random coil, β-turn and extended strand predominates. Transmembrane region prediction showed that both the proteins were soluble form. As RNA polymerase II of Phoenix pusilla has only 27aminoacid residues, 3D structure has to be predicted with other logarithmic tool and so 30Sribosomal protein 3D structure was predicted with Swiss model server.