Abies delavayi subsp. fansipanensis is classified as a highly endangered plant in the Vietnam Red Data Book (2007) and a critically endangered species in IUCN red list (2012). This species distributed at the altitudes of 2600-2680 m and 2750-2950 m above sea level (a.s.l) on Fansipan-mountain, Lao Cai province, Vietnam. However, to date there is still a lack of information on the bio-ecological and genetics characteristics of Abies delavayi subsp. fansipanensis indifferent altitudinal conditions, which helps to conserve and promote this precious genetic resource in Vietnam. In this study, climate conditions, soil property, vegetation and genetic structure of two populations of Abies delavayi subsp. fansipanensis distributed in two altitudinal belts on Fansipan-mountain were investigated. The research results have shown that Abies delavayi subsp. fansipanensis is distributed in the ecological conditions including temperature: 1.6-29.3^°C, rainfall: 26.8-500 mm, humidity: 65%-95%, sunshine: 90-130 h sunshine, pH: 4-5, and the total organic carbon value 34-73%. The importance value index (IVI) and the correlation coefficient of the relationship of tree height and diameter at breast height values of Abies delavayi subsp. fansipanensis distributed in the altitudes of 2600-2680 m a.s.l. were 4.72% and 0.2749, while those of this species in the altitudes of 2750-2950 m a.s.l. were 42.24% and 0.6824, respectively. The DNA analysisof Abies delavayi subsp. fansipanensis also indicated that the genome of individuals in the higher altitude is more diverse than those lived in the lower altitude. This is the first study of the bio-ecological and genetic structure characteristics of Abies delavayi subsp. fansipanensis distributed on Fansipan-mountain. The study provides valuable data for proposing solutions to conserve and promote this rare genetic resource for Vietnam as well as for the world.