A study was designed to isolate and identify the endophytic mycobiota in leaves and twigs of Rubus spectabilis and R. parviflorus, the long-term goal being biological control of these plants with endophytes. Endophytic fungi were isolated from healthy-looking leaves and twigs collected from each species on Vancouver Island, British Columbia, Canada. More than 90% of the leaves of both species were colonised by endophytes. In addition, one third of the twig samples of each species were also colonised. Most isolates belonged to Phomopsis, and five species were identified and characterised according to morphology of the cultures and fructification structures. All Phomopsis species occurred on both Rubus species, but, one primarily colonised R. parviflorus, whereas another preferentially colonised R. spectabilis. The suitability of the isolated endophytes to inhibit growth of R. spectabilis and R. parviflorus, which compete with conifers in reforestation sites, is discussed.