Chitosan has been shown to be effective in regulating progenitor salivary tissue morphogenesis, however, the specificity of chitosan effects remains unclear. To assess the regulatory ability of chitosan in salivary gland morphogenesis, progenitor salivary tissue from embryonal submandibular gland (SMG) was cultured in chitosan-containing medium. It was found that soluble chitosan was able to promote SMG branching in a dose-dependent manner. The effect was chitosan-specific and was not reproduced by substrates with similar chemical structures or other polymeric molecules of natural or synthetic origin. Furthermore, the branch-promoting effects were molecular weight-dependent. In addition, following digestion with lysozyme, chitinase, or chitosanase, digested chitosan was unable to reproduce the similar effects. In all, this study clarifies the specificity and preferential activity of chitosan in enhancing branching morphogenesis of progenitor salivary tissue and highlights its potential utility for application in salivary tissue regeneration.