Recently introduced parasites are predicted to cause more severe infections because of a lack of host-parasite co-evolution. When new parasites co-occur with similar parasites they may compete for resources within a host, with mixed species infections potentially resulting in antagonistic, synergistic or additive effects. We tested Ostrea chilensis flat oysters in New Zealand for infections by two species of haplosporidian oyster parasites. Bonamia exitiosa is an endemic parasite to New Zealand, whereas Bonamia ostreae is an introduced species first detected in New Zealand in 2015. We investigated the infection intensity of each parasite by estimating gene copy numbers using species-specific digital droplet PCR (ddPCR) across Bonamia spp. allopatric and sympatric ranges. Our results showed that B. ostreae had significantly higher gene copy numbers than B. exitiosa. However, concurrent infections of both Bonamia parasites had similar intensities (based on gene copy number) to single-species infections, with no detectable interactive effects. Collectively, the results indicate that B. ostreae remains a significant risk to O. chilensis, although coinfections may not exacerbate disease. This study demonstrates the value of ddPCR screening and the importance of considering evolutionary ecology in the management of commercially important marine diseases.