Horticulture program consists of four sub-programs namely Fruits and Nuts, Vegetable, Medicinal and Aromatic Plants and Mushroom program. The core objective of the horticulture program is to help develop strategies to attain self sufficiency and commercialization of horticulture crops. The activities are focused mainly on the development and promotion of sub-tropical and warm temperate fruits and vegetables for mid altitude areas. Under medicinal and aromatic plants(MAP) program, study on important MAP plants are undertaken while in the case of mushroom program, it is purely developmental in nature wherein technical support is provided for cultivation of two types of mushroom namely shiitake (Lentinula edodes) and oyster (Pleurotus sp.).

The horticulture sector undertakes basic and applied research and outreach activities on horticulture crops. The research part is mainly on the development of varieties of commercial oriented horticulture crops, and on crop management practices for crop production and management. Different lines and varieties of commercial oriented horticulture crops are introduced and evaluated (on-station and on-farm). The lines/varieties performing well are finally released for cultivation by the growers. The collection, characterization and performance evaluation of local germplasm is also undertaken to mainly identify valuable traits like pest and disease resistance, drought tolerance and nutritional content. The local germplasm collection and maintenance are also to increase the genetic diversity and for use in future breeding programs for development of desirable traits. The study of local germplasm is also given importance because of cultural values attached with some cultivars. The development of production technology for horticulture crops is mainly to increase yield and improve quality through research in proper and efficient nutrient, water and pest management practices.

Horticulture outreach activities or outreach program has become a major activity ever since the development mandate was attached to the research centres in the year 2008.  Horticulture outreach activities is primarily focused on promotion of improved fruit crop cultivation through production and distribution of seedlings, systematic training on crop management practices in collaboration with the  district agriculture office of the five west central districts. The positive feedbacks has resulted in research centres to step up the outreach program further. With the start of the five years (2016-2020) Technical Co-operation Integrated Horticulture Promotion Project (IHPP) with the Japan International Co-operation Agency (JICA), Government of Japan, the outreach activities are going to intensify. Ground works like seed and seedling production are already underway.

The horticulture sector has so far released 14 fruit crops and 25 vegetables varieties.  The horticulture sector provides technical support to five districts of the west central region namely Gasa, Punakha, Wangdiphodrang, Tsirang and Dagana.