The fabrication of 3C‐SiC and 6H‐SiC pn junction diodes, grown side by side on low‐tilt‐angle 6H‐SiC substrates via a chemical vapor deposition (CVD) process, has recently been reported. Admittance spectroscopy and deep‐level transient spectroscopy (DLTS) measurements were made on one of these diodes to compare the defect structure of 3C‐ and 6H‐SiC CVD epitaxial layers grown under the same conditions. The 6H‐SiC layers revealed a single minority carrier level and a deeper broad majority carrier peak. The minority level is due to the boron‐related D center, whereas the broad majority level was identified as a double peak by a DLTS simulation. DLTS measurements on the 3C‐SiC layers revealed only one deep level impurity consistent with the boron‐related D center. Shallow donor levels observed using admittance spectroscopy correspond with the known shallow nitrogen donor in both 3C‐ and 6H‐SiC epitaxial layers. This confirms that both 3C‐ and 6H‐SiC polytypes were simultaneously formed on the same 6H-SiC substrate.