The epidemiology of influenza in the North American swine population has changed since the emergence of a triple-reassortant H3N2 influenza virus. Although seen previously in North America, the Ontario swine population had likely been free of viruses of the reassortant H3N2 lineage until 2005. The objective of this study was to investigate the frequency and distribution of exposure to H1N1 and H3N2 subtypes in the Ontario finisher pig population prior to and after the H3N2 outbreak that occurred in 2005. This included investigating prevalence and spatial distribution of positive herds, assessing proportion of random variation at different hierarchical levels, and evaluating selected demographic factors and management procedures as potential risk factors. In total, 919 and 978 sera collected in cross-sectional studies from 46 and 49 finisher herds in 2004 and 2005 were tested by a H1N1 subtype-specific and a H3N2 subtype-specific commercial ELISA. For the H1N1 subtype, the point prevalence of positive herds (>3 reactors) was 19.5% and 30.6% in 2004 and 2005, respectively. For the H3N2 subtype the point prevalence of positive herds (>3 reactors) was 6.5% and 40.8% in 2004 and 2005, respectively. Sera from 2004 that were positive on H3N2 ELISA did not cross-react with any of the H3N2 variants used as antigen on a sequential HI test. Only herds positive for H3N2 subtype in 2005 clustered in space (P<0.01). The H1N1 status in 2005 was associated with the H1N1 status in 2004, and with reported distance to the nearest herd. The H3N2 status in 2005 was associated with reported distance to the nearest herd and a type of replacement gilt source. For H3N2, distance seemed to be important even after controlling for type of gilt source. Most variability in seropositivity was between herds with little variability between pens. This study confirms that in 2005, the epidemic H3N2 subtype co-circulated with endemic H1N1 subtype in the Ontario finisher herds. We concluded that in Ontario, the endemic H1N1 subtype was likely maintained through circulation within herds and sites with common flow. Whereas the transmission of epidemic H3N2 subtype was attributed to local spread, which could include different modes of direct, indirect, and airborne transmission. We emphasize the importance of establishing routine monitoring systems that would allow using molecular tools, and maintaining serum banks as a useful resource for retrospective comparisons.