The paper presents the application of hidden Markov models (HMM) in the analysis of the linguistic microdifferentiation of 48 reproductively isolated populations in the Eastern Adriatic. The mathematical method is described in detail when applied for the recognition of the two main dialects (cakavian and stokavian) present in the investigated area, using two distinguished HMM. The resulting classification of villages is compared to those of the clustering methods applied previously for the same purpose.