Development of nano-electronics, basically depends on the fact that how quickly the practical idea of fabricating nanoswitches is realized. It has already been proposed that the electronic switches from single wall carbon nanotubes could be obtained by adding an odd member ring in the hexagonal net of the tube [1,2]. However, it is much difficult to control the position and number of such a ring. Recently it was proposed that such switches could also be made by adding a layer of one type of tube on the top of the other such that both the tubes have different metallicities. This is how the idea of nanometric heterojunctions comes into existence. Nanometric type heterojunctions are supposed to be made by connecting the nanotubes of different metallicities. The basic advantage of Nanometric heterojunctions is the fact that their electronic properties are easier to control since these properties depends on their composition only and not on the helicity and radius of the tube, for example: The gaps for BC3 and BC2N nanotubes are approximately 0.5 and 2.0eV [3,4]. These heterojunctions have a number of proposed nanotechnological applications. In the present paper we report a detailed analysis of C/BN nano-heterojunctions. Survey of literature on BCN nanotubes reveals that these are the materials in which carbon atoms in carbon nanotubes are partially substituted by boron and nitrogen atoms such that both, the random substitution as well as the ordered layers of BN and C2 are possible [5,6]. Total energy calculations show that two dimensional BC2N tends to form strips or pure islands of BN and C [7]. Owing to these facts one can propose that a BC2N nano heterojunction could be realized by connecting carbon and boron nitride nanotubes (equal number of rings of both the tubes as shown in Fig. 1.)figureFig. 1. BC2N nano-heterojunctions of (10,10) armchair (Left) and (10,0) Zigzag (Right). Carbon atoms are in golden spheres, while red and green are B and N atoms, respectively.In the present work we examined the isolated junctions of various armchair and zigzag configurations of nanotubes, to obtain their phonon spectrums. A lattice dynamical model is used for phonon modes calculations and the zonefolding scheme is employed for the Brillouin zone definition. A detailed comparative analysis of vibrational mode for varying C/BN concentrations at the junctions, is presented in the paper. Calculated Raman modes are in good agreement with those reported experimentally for different concentrations of B, C and N in nanotubes [8]. It is observed that the peaks in the spectrum get broadened with the increase in BN concentration at the junction. It is also observed that Raman modes are least affected if C/BN ratio is kept constant even though the radius changes, which means that the peaks of Raman spectra does not seem to be affected by the radius of the nanotube.