This study was designed to appraise the challenges of agrobiodiversity degradation in Niger Delta region of Nigeria. One research question and one hypothesis were formulated to guide the study. A total of 552 respondents comprising rural farmers, and forestry officers were involved in the study. Respondents were drawn from all Niger Delta States in Nigeria. These included, Abia, Akwa Ibom, Bayelsa, Cross River, Delta, Edo, Imo, and Rivers States. The data were obtained through a structured questionnaire and analyzed with the use of percentage and chi-square as statistical tools. The findings of the study ascertained the basic challenges of agrobiodiversity degradation in the region to include intensive resource exploitation and extensive alteration of habitats, neglect of agrobiodiversity conservation practices, blueprint approach to development whereby monoculture systems and uniform technologies are promoted, quest for the transnational corporations that market agricultural inputs and process food and fibres for commercial profits and uncontrolled over-production, inequitable access to and control over land, water, trees and genetic resources of the part of local people, market pressures, under-valuation of agricultural biodiversity, pests and disease invasion, population pressure, deforestation, flooding, poverty and oil spillage among others. It was recommended among others that the governments of Niger Delta states should develop innovative funding mechanisms to support agrobiodiversity conservation programmes in the region by collecting special taxes on agricultural resources such as timber extraction, wood trading, trade in crop and livestock products, and other activities connected with the sector.