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Background  The ethnic groups in Gilgit-Baltistan have been utilizing local resources in their centuries-old traditional healing system. Most tribes within these ethnic groups still rely on traditional healing systems. We aim to understand the current status, uses, and abundance of medicinal plants, associated traditional knowledge, and trade.    Materials and methods  The study incorporated over 300 local community members (70% men and 30% women) in focused group discussions, semi-structured interviews, and homework assignments for 8th to 12th grade students to document traditional knowledge (TK) in six districts in Northeast Pakistan. We calculated various indices such as informant consensus factor, use value, relative frequency of citation, and CoKriging. These indices, along with repetitively used medicinal plants, were used to analyze differences in studied locations.    Results  Most of the community members still rely on traditional medication in the study areas. However, we found the highest number of medicinal plants used in Skardu and Gilgit compared to other districts and these two districts also represent trade centers and a highly populated area regarding medicinal plants. Results indicate connection amongst the surveyed villages signifying mixing of knowledge from different sources, with certain areas more influenced by traditional Chinese medicine and others more by Ayurveda and Unani.    Conclusion  TK is mostly retained with elder community members; however, those directly linked with market value chain retain rich knowledge on traditional use of the medicinal plants from the region. Major trade centers in the region also coincide with a high density of medicinal plant occurrence, knowledge, and higher utilization. Therefore, with the increasing trade in medicinal plant in the region, there is potential for rejuvenation of this knowledge and of plant use in the region.    Electronic supplementary material  The online version of this article (10.1186/s13002-018-0281-0) contains supplementary material, which is available to authorized users.

Regional trade of medicinal plants has facilitated the retention of traditional knowledge: case study in Gilgit-Baltistan Pakistan