Sphaerothecum destruens is an obligate intracellular parasite with the potential to cause high mortalities and spawning inhibition in the endangered cyprinid Leucaspius delineatus. We investigated the influence of L. delineatus’s reproductive state on the prevalence and infection level of S. destruens. A novel real time quantitative polymerarse chain reaction (qPCR) was developed to determine S. destruens’ prevalence and infection level. These parameters were quantified and compared in reproductive and non-reproductive L. delineatus. The detection limit of the S. destruens specific qPCR was determined to be 1 pg of purified S. destruens genomic DNA. Following cohabitation in the lab, reproductive L. delineatus had a significantly higher S. destruens prevalence (P<0·05) and infection levels (P<0·01) compared to non-reproductive L. delineatus. S. destruens prevalence was 19% (n=40) in non-reproductive L. delineatus and 41% (n=32) in reproductive L. delineatus. However, there was no difference in S. destruens prevalence in reproductive and non-reproductive fish under field conditions. Mean infection levels were 18 and 99 pg S. destruens DNA per 250 ng L. delineatus DNA for non-reproductive and reproductive L. delineatus respectively. The present work indicates that S. destruens infection in L. delineatus can be influenced by the latter's reproductive state and provides further support for the potential adverse impact of S. destruens on the conservation of L. delineatus populations.