Abstract: Avicennia marina is mangrove plant. Genetic diversity and genetic differentiation were measured with the assay of vertical slab polyacrylamide gel electrophoresis in Avicennia marina populations.and climate and chemistry physical as characteristic of soils were analyzed in sampling sites of 5 Avicennia marian populations. The ecological analyses of genetic variation and ecological differentiation of Avicennia marina populations were studied. The environmental factors have a significant relation with 4 alleles including Aat-1A,Aat-1D，Me-1B，Me-1C,showing that the environmental factors which relate with the alleles have selective pressure on the 4 alleles,and the 4 alleles varied with the environmental factors.