Context Controlled pollination is an important technique for maintaining intraspecific diversity in integrated plant conservation practices, particularly in genera such as Rhododendron, where open pollination usually produces hybrids with unknown paternal lineages. Aims This study investigated the capacity for viable seed set from self- and intraspecific cross-pollination for Rhododendron taxa in different categories of the International Union for Conservation of Nature (IUCN) Red List, to guide conservation management of threatened species in botanic garden collections. Methods The following five taxa of subsection Maddenia were studied: R. dalhousiae var. dalhousiae (Least Concern), R. dalhousiae var. rhabdotum (Vulnerable), R. lindleyi (Least Concern), R. nuttallii (Near Threatened), and R. excellens (Vulnerable). Controlled pollination was performed on selected garden accessions, and seed germination was tested at an alternating temperature regime of 15/25°C, 8 h photoperiod, and ~6 μmol m−2 s−1 photosynthetic photon flux density (PPFD). Key results Intraspecific compatibilities varied among different taxa and between self- and outcross treatments. X-ray images for Rhododendron seeds showed low capacity to predict seed germination. Neither X-ray scan nor fungicide (Ridomil) treatment showed any adverse impact on seed germination, which has positive implications for seed-banking and subsequent raising of Rhododendron seedlings. Conclusions Controlled intraspecific pollination can be used to maintain diversity of ex situ accessions for selected Rhododendron species. However, the zero or low compatibility demonstrated in some species, such as R. excellens, suggests that these species may require a different approach. Implications Intraspecific pollination should be evaluated for each Rhododendron species before a propagation program is initiated in ex situ conservation.