Hoverflies are essential to ecosystems, with adults serving as important pollinators and larvae preying on plant-feeding insects or recycling nutrients. Species like Sphaerophoria rueppellii are used in biocontrol programs to target aphid pests. To enhance these programs, markers can be used in a mark-release-recapture (MRR) method to track hoverfly feeding and oviposition sites. Effective markers must be persistent and not harm the hoverflies' vital functions. This study evaluated three marking methods for S. rueppellii: rubidium (RbCl), fluorescein, and fluorescent dust. Laboratory experiments assessed the effects of these markers on female hoverfly fecundity, mating behavior and marking persistence. Results showed no significant differences in egg-laying or survival time between marked and unmarked females. Rubidium and fluorescein did not affect mating behavior, but dust-treated females mated significantly less than untreated females. In terms of marking persistence, rubidium and fluorescent dusts remained detectable throughout the hoverflies' adult lifespan, while fluorescein markings faded within 24 h. Fluorescent dusts were easy-to-use, durable, and cost-effective, but careful application and further study are needed to avoid potential effects on insect activity and mating ability. Fluorescein showed no adverse effects on insect biology, was economical and quick to apply, but had short persistence, making it unsuitable for long-term field studies. Rubidium was harmless to insects and detectable for long periods, but its detection required financial investment, time, and specialized equipment. This research provides valuable insights into the potential of hoverflies as biocontrol agents and offers new tools for their effective management in agricultural settings.