Preaxial polydactyly (PPD) is congenital hand malformation characterized by the duplication of digit. Herein, wescan the genome-wide SNPs for a large Chinese family with PPD-II/III. We employ the refined IBD algorithm toidentify the identity-by-decent (IBD) segments and compare the frequency among the patients and normalrelatives. A total of 72 markers of 0.01 percentile of the permutation are identified as the peak signals. Among ofthem, 57markers locate on chromosome 7q36 which is associated with PPD. Further analyses refine the mapping ofcandidate region in chromosome 7q36 into two 380 Kb fragments within LMBR1 and SHH respectively. IBDapproach is a suitable method for mapping causal gene of human disease. Target-enrichment sequencing as wellas functional experiments are required to illustrate the pathogenic mechanisms for PPD in the future.