This paper proposes phoneme clustering methods for multilingual language identification (LID) on a mixed-language corpus. A one-pass multilingual automated speech recognition (ASR) system converts spoken utterances into occurrences of phone sequences. Hidden Markov models were employed to train multilingual acoustic models that handle multiple languages within an utterance. Two phoneme clustering methods were explored to derive the most appropriate phoneme similarities between the target languages. Ultimately a supervised machine learning technique was employed to learn the language transition of the phonotactic information and engage the support vector machine (SVM) models to classify phoneme occurrences. The system performance was evaluated on mixed-language speech corpus for two South African languages (Sepedi and English) using the phone error rate (PER) and LID classification accuracy separately. We show that multilingual ASR which fed directly to the LID system has a direct impact on LID accuracy. Our proposed system has achieved an acceptable phone recognition and classification accuracy in mixed-language speech and monolingual speech (i.e. either Sepedi or English). Data-driven, and knowledge-driven phoneme clustering methods improve ASR and LID for code-switched speech. The data-driven method obtained the PER of 5.1% and LID classification accuracy of 94.5% when the acoustic models are trained with 64 Gaussian mixtures per state.