Native defects in InxGa1–xN grown by plasma-assisted molecular beam epitaxy were probed by a monoenergetic positron beam. Doppler broadening spectra of the annihilation radiation were measured, and these were compared with results obtained using first-principles calculation. The defect concentration increased with increasing In composition x and reached the maximum at x = 0.44∼0.56. A clear correlation between the line-width of photoluminescence and the defect concentration was obtained. The major defect species detected by positron annihilation was identified as cation vacancies coupled with multiple nitrogen vacancies (VNs), and their introduction mechanism is discussed in terms of the strain energy due to bond-length/angle distortions and the suppression of the VN formation energy by neighboring In atoms.