Genetic diversity of Lianjiang wild population (LJWN), Lianjiang cultured population (LJYN), Changle cultured population (CLYN), Guangxi wild population (GXWN) of Babylonia lutosa (Lamer) was analyzed by amplified fragment length polymorphisms (AFLP). For the assessment, total 908 bands were generated from four populations using 11 different primer combinations, 684 (75.33%) were polymorphic fragments of which 224 (24.67%) are shared by the four populations. Genetic diversity index analysis showed, the effective number of alleles, the average number of alleles, Shannon’s diversity index and average heterozygosity were 1.500 6, 1.974 0, 0.464 7, 0.303 4, respectively; Nei’s genetic distance and genetic similarity coefficient were ranged from 0.128 4 to 0.180 6 and 0.834 8 to 0.879 5, indicating relatively rich genetic diversity and high genetic similarity among the four populations of Babylonia lutosa (Lamer).Results of analysis of molecular variance (AMOVA) and assignment test revealed 83.49% variation within population, 14.65% variation from region difference and 1.86% variation among the four populations. Genetic variance GST and NM were 0.195 4 and 2.058 6 among four population groups indicating that the gene exchange level is very low. The analysis results of UPGMA and PCA showed that the nearest genetic distance exists between CLYN population cultured cultured cultured cultured populationand GXWN population. Genetic distance between LJWN population and other 3 populations was the farthest.