Pulsed field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) methods were applied for molecular typing of 130 Mannheimia (Pasteurella) haemolytica serotype A1 isolates obtained from 13 prefectures in Japan. These isolates were divided into 15 ApaI PFGE profiles that formed six distinct clusters (clusters A–F). Fifty-three (40·7%) isolates were classified in cluster B, and 20·0, 13·8, 12·3, 6·9 and 6·1% of isolates were in clusters E, A, F, D and C, respectively. The isolates of cluster B were differentiated into seven subtypes (B1–B7) and subtype B5 contained 63% (34/53) of isolates. RAPD revealed four banding patterns (types I–IV), and among 130 isolates 60·7% (79/130) of isolates were RAPD type I. All of the RAPD type I isolates were grouped into clusters A–C by PFGE. There was no relationship between molecular typing and geographic origin of these isolates. These results indicate that isolates of M. haemolytica A1 strain with various molecular profiles have already spread in Japan and may have caused sporadic infections.