Lake Victoria region has the highest HIV prevalence in East Africa due to concentration of commercial farms, fishing and mining that escalate social dynamic interactions. High rates of HIV transmission and poor working conditions further amplify the risk of TB in the region. Local populations in the area have opted different alternatives among which medicinal plants are popular for managing health conditions related to the respiratory diseases. Consequently, selective consumerism of plants for managing respiratory diseases profoundly affects diversity of priority medicinal plants. Detection of the effect of selective consumerism to the preferred plants in-situ is not instantaneous unless much focused approach is employed. In this study, an ethnobotanical assessment criterion was used to assess and identify conservation status for most useful plants. To achieve this, open ended questionnaires and focus group discussions were used for collecting ethnobotanical information from 37 traditional health practitioners on the use of herbal remedies against various respiratory diseases. Guideline by the international union for conservation of nature (IUCN) medicinal plant specialist group was used to assess qualitative distribution of indicator species through ethnographic methods. A protocol for conservation assessment management plan was used to prioritize limited number of species for ex-situ conservation. Ethnobotanical parameters, value–index and legislation-index were used for scoring in two-dimensional manner. Scoring analysis highly prioritized non-timber plants including Rubia cordifolia, Crassocephalum manii and Pavetta crassipes for conservation over timber species. From the findings, an ethnobotanical assessment criterion is recommended for total conservation of all plant categories in the wild including the often neglected non timber plant species.