Changes in the structure of managed red pine forests in Wisconsin caused by interacting root- and stem-colonizing insects are associated with increased abundance of the blacklegged tick, Ixodes scapularis Say, in comparison with nonimpacted stands. However, the frequency and variability of the occurrence of tick-borne pathogens in this coniferous forest type across Wisconsin is unknown. Red pine forests were surveyed from 2009 to 2013 to determine the prevalence of Borrelia burgdorferi and Anaplasma phagocytophilum in questing I. scapularis nymphs. Polymerase chain reaction analysis revealed geographical differences in the nymphal infection prevalence (NIP) of these pathogens in red pine forests. In the Kettle Moraine State Forest (KMSF) in southeastern Wisconsin, NIP of B. burgdorferi across all years was 35% (range of 14.5–53.0%). At the Black River State Forest (BRSF) in western Wisconsin, NIP of B. burgdorferi across all years was 26% (range of 10.9–35.5%). Differences in NIP of B. burgdorferi between KMSF and BRSF were statistically significant for 2010 and 2011 and for all years combined (P < 0.05). NIP of A. phagocytophilum (human agent) averaged 9% (range of 4.6–15.8%) at KMSF and 3% (range of 0–6.4%) at BRSF, and was significantly different between the sites for all years combined (P < 0.05). Differences in coinfection of B. burgdorferi and A. phagocytophilum were not statistically significant between KMSF and BRSF, with an average of 3.4% (range of 1.7–10.5%) and 2.5% (range of 0–5.5%), respectively. In 2013, the density of infected nymphs in KMSF and BRSF was 14 and 30 per 1000m², respectively, among the highest ever recorded for the state. Differences in the density of nymphs and NIP among sites were neither correlated with environmental factors nor time since tick colonization. These results document significant unexplained variation in tick-borne pathogens between coniferous forests in Wisconsin that warrants further study.