For a large corpus of time-aligned data, HMM based approaches are most widely used for automatic segmentation, providing a consistent and accurate phone labeling scheme. There are two methods for training in HMM. Flat starting method has a property that human interference is minimized but it has low accuracy. Bootstrap method has a high accuracy, but it has a defect that manual segmentation is required In this paper, a new algorithm is proposed to minimize manual work and to improve the performance of automatic segmentation. At first phase, voiced, unvoiced and silence classification is performed for each speech data frame. At second phase, the phoneme sequence is aligned dynamically to the voiced/unvoiced/silence sequence according to the acoustic phonetic rules. Finally, using these segmented speech data as a bootstrap, phoneme model parameters based on HMM are trained. For the performance test, hand labeled ETRI speech DB was used. The experiment results showed that our algorithm achieved 10% improvement of segmentation accuracy within 20 ms tolerable error range. Especially for the unvoiced consonants, it showed 30% improvement.