<p>The application of flow cytometry (FCM) in plant sciences has significantly advanced the study of karyological and cytogenetic aspects across diverse plant groups. This method also holds substantial potential for detecting critical evolutionary processes such as hybridization and introgression, which can threaten the genomic integrity of affected species and, in extreme cases, lead to extinction in rare and small populations. However, the use of FCM for hybrid detection and its implications for conservation efforts have largely been overlooked. This study aims to demonstrate the practical application of this method, summarize its advantages and limitations, and propose solutions for conservation biologists. We examined several pairs of related plant species, at least one of which was endangered and showed morphological indications of hybridization, mostly supported by previous investigations. In all studied pairs, we identified cytotypes with genome sizes intermediate between those of the potential parental taxa. Hybridization was evidenced in all heteroploid model systems except for <i>Aconitum</i>, where polyploids may arise from the fusion of reduced and unreduced gametes of the same taxon. Similar results confirming hybridization were found in pairs of homoploid taxa, where however, transitional cytotypes exhibited variability, creating a continuum within the spectrum of parental genome sizes. By discussing these results in conjunction with the methodological shortcomings and offering best practice recommendations, we demonstrate that FCM can effectively provide initial insights into the presence of potential hybrids in endangered plant taxa, thus establishing it as a valuable tool for nature conservation efforts.</p>