Probiotic functional foods are known to have various functional effects such as intestinal regulation, modulation of immune system, reduction of allergies, and lowering of cholesterol. The purpose of this study was to select probiotic strain that is most suitable for freeze-dried coffee for the development of functional coffee products. The survival rate of probiotics, at drinking condition of coffee, at acid, at bile and after freeze-dried in coffee were measured on 1 strain isolated from commercial freeze-dried coffee, 8 strains used as fermented milk starter, 1 Bifidobacterium and 1 Bacillus coagulans. Bacillus coagulans showed the highest survival rate from 2.4×107 cfu/g to 2.0×107 cfu/g especially after freeze-drying. The results at drinking condition of coffee, at acid tolerance, at bile tolerance and at storage test showed significantly better survival rate of Bacillus coagulans than that of control (Lactobacillus casei). Especially, Bacillus coagulans showed 3.8-fold higher survival rate at acid tolerance (pH 1, 120 minutes) than control. Thus, the lactic acid-producing Bacillus coagulans is characterized as a probiotic strain suitable for functional coffee formulation and commercialization.