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This study assessed woody species diversity in different ecological zones of Taraba State. The objectives were to determine the abundance, distribution and comparison of woody species diversity in order to protect and monitor the forest ecosystems. Data were obtained through the woody species survey, and the study area was stratified into three ecological zones and two protected areas. Five plots each measuring 50 × 50 m were sampled in each protected area. Data were analysed using descriptive and inferential statistics such as frequency, ANOVA and LSD. A total of 3760 individual woody stands were recorded in the study. A total of 60, 34 and 32 species were also encontered in Montane Forest, Southern and Northern Guinea Savanna, respectively. Ngel Nyaki Forest Reserve had the highest species richness value (49) followed by Wasaji Forest Reserve (26) while Gashaka Gumti National Park had the lowest value (13). The Shannon diversity index of woody species in the protected areas were 2.96, 2.90, 2.48, 2.20, 2.46, 2.48 and 2.53 in Ngel Nyaki, Wasaji, Baissa, Jen Giginya and Gashaka, respectively while their corresponding evenness values were 0.76, 0.89, 0.77, 0.79, 0.86 and 0.76, respectively. The higher species richness and Shannon Wiener diversity indices can be attributed to low disturbance and habitat conditions of the ecosystems. While the lower diversity indices could be as a result of overexploitation of woody species. Sorensen’s similarity indices between the ecological zones were 0.11, 0.01 and 0.84 for Montane Forest, Southern Guinea Savanna and Northern Guinea Savanna, respectively. Species diversity differs significantly (P<0.05) among the ecological zones and protected areas. Therefore, more priority areas should be identified and conserved for sustainability.