The main objective of this study was to identify the circulating strains of Mycobacterium avium subspecies paratuberculosis (Map) in fecal isolates obtained from dairy goat (N = 29 farms) and dairy sheep (N = 21 farms) populations in Ontario, Canada. Further subtyping was performed to determine if there was adequate diversity between strains that could be used to establish Map transmission patterns. Type C was the dominant strain of Map isolates (95.2%) identified in dairy goats (n = 21). Sub-typing of the Type C strains, based on variable number tandem repeats (VNTR) and mycobacterial interspersed repetitive units, identified 3 VNTR types: INMV 1 (n = 10), INMV 2 (n = 10), and a type not previously identified (n = 1). Only 2 sheep isolates could be identified; both were Type S, sub-type III. Current typing methods demonstrate little Map diversity in the dairy goat population and are therefore of limited use to investigate infection patterns.