Mixed trypanosomatid infections (a simultaneous presence of two or more parasites in the same host) have long been suspected to represent an obstacle for recovering cultures that would faithfully represent original species descriptions. However, without the means to directly compare the parasites in the host and in culture, this would remain just a possibility. Here we have used PCR-based genotyping of spliced leader RNA gene repeats to analyse several novel species of insect trypanosomatids isolated from heteropteran hosts and to compare them with the parasites that had been detected in the gut smears of the same hosts. We have found that, whereas the original infections were dominated by some blastocrithidia-like parasites, most of the respective axenic cultures contained novel species of Crithidia and Leptomonas. Therefore, we concluded that, in each case, this replacement was caused by differences in cultivation properties between the original predominant blastocrithidia and the less fastidious parasite that was later recovered in culture. The properties of the new organisms, including their morphology and ultrastructure, as well as their phylogenetic affinities within the family, were investigated and used to describe five novel species.