Technical Abstract: Superinfection occurs when a second, genetically distinct strain infects a host that has already mounted an immune response to a primary strain. For antigenically variant pathogens, the primary strain itself expresses a broad diversity of variants over time. Thus successful superinfection would require that the secondary strain express a unique set of variants. We tested this hypothesis under conditions of natural transmission in both temperate and tropical regions where, respectively, single strain infections and strain superinfections of the tick-borne pathogen Anaplasma marginale predominate. Our conclusion that strain superinfection is associated with a significant increase in variant diversity is supported by progressive analysis of variant composition: i) animals with naturally acquired superinfection had a statistically significantly greater number of unique variant sequences as compared to animals either experimentally infected with single strains or infected with a single strain naturally; ii) the greater number of unique sequences reflected a statistically significant increase in primary structural diversity in the superinfected animals; and iii) the increase in primary structural diversity reflected increased combinations of the newly identified hypervariable micro-domains. The role of population immunity in establishing temporal and spatial patterns of infection and disease has been well-established. The results of the present study, which examined strain structure under conditions of natural transmission and population immunity, support that high levels of endemicity also drive pathogen divergence towards greater strain diversity.