The primary objective of this study was to determine, at the lung level, whether single or multiple clones of Mannheimia haemolytica are present within a pen during a bovine respiratory disease (BRD) episode. A secondary objective was to assess whether M. haemolytica isolates obtained from nasal swabs (NS) are identical to those isolated deeper within the respiratory tract. Sixteen BRD episodes that naturally occurred in 12 pens of eight to 12 bulls (n = 112) newly-received at three fattening operations were investigated. One hundred and seventy five M. haemolytica isolates were collected from 239 pairs of trans-tracheal aspirations (TTA) and NS performed during these 16 BRD episodes. M. haemolytica isolates were characterized by pulsed-field gel electrophoresis (PFGE). PFGE types obtained from NS and TTA were then compared. M. haemolytica was isolated during 14 BRD episodes. Two to three different clones of M. haemolytica were recovered during 10 episodes whereas only one clone was recovered in four episodes. A moderate agreement (kappa = 0.50) between NS and TTA for M. haemolytica isolation was observed. Identical PFGE types were only observed in 77% of matched NS-TTA pairs. The significant within-pen diversity of M. haemolytica during BRD episodes indicates that the disease is not primarily due to the spread of a single virulent clone among cattle and highlights the importance of predisposing factors that enable the resident flora to overcome the cattle's immune system. The results also demonstrate that isolates recovered from NS are not always representative of the isolates present deeper within the respiratory tract