This article describes a method for differentiating two types of horse gaits: walk and trot. Recognition of gait types is significant for different research branches. It is important in animal behavior analysis, gait and stride timing analysis, lameness detection, sports such as horse trotting and identifying opportunities for the use of horses. Research described in this article concerns detection of horse gait type on the basis of acceleration measurement with the use of inertial motion capture system. Two 6 DoF motion trackers were used for recording vertical acceleration of a horse trunk at the withers and at the lumbo-sacral junction. Developed method for gait type differentiation uses discrete Fourier transform and the analysis of local maximums of Fourier magnitude spectrum with LDA. Presented research results shows that it is possible to distinguish between two gait types mentioned above in automatic manner.