Gracilaria lemaneiformis is important economic red algae for its high production of agarose. It is also has very important roles such as an important role in bioremediation and the inhibition of algae blooming. So the research on G. lemaneiformis nowadays needs attentions to paid. For the unique lifecycle of G. lemaneiformis, different phases and sex of populations can be found in the same time and same places. This study was aimed on the difference of genetic diversity between the haploid and diploid populations of G. lemaneiformis based on AFLP technique. G. lemaneiformis of different phases of the lifecycle were collected, and AFLP was carried on with 7 primer combinations. The result was analyzed based on the DNA finger map. Inter- and intra-population genetic diversity of haploid and diploid Gracilaria lemaneiformis samples from Zhanshan Bay and Taiwan Road of Qingdao were analyzed.The Na, Ne, H, I and P was 1.1699, 1.095, 0.0582 0.0884, and 16.99% for haploid population and 1.333, 1.2270, 0.1297, 0.1908 and 33.33% for diploid population of Zhanshan Bay, respectively. The above genetic index was 1.1373, 1.0899, 0.0504, 0.0746 and 13.73% for haploid, and 1.2092, 1.1386, 0.0825, 0.1219 and 20.92% for diploid of Taiwan Road, respectively. The above mean genetic index of the haploid populations for 1.2092,1.0971,H 0.0576,0.0896,20.92%, and the above mean genetic index of the diploid populations for 1.4248,1.3682,0.1946,0.2756,42.48%. Genetic diversity between different phases was revealed by the comparison of genetic index. The diploid showed higher genetic variation than haploid from the same geographical population. The genetic diversity influenced by phases was stronger than those from geographical or environmental factors. The Ht, Gst and Nm of haploid population between Zhanshan Bay and Taiwan Road was 0.0581, 0.0669 and 6.9683 respectively, showed great difference with those of diploid population, with Ht 0.1799, Gst 0.3271 and Nm1.0285. The two haploid populations could be considered as one large random population for its high gene flow 6.9683; there was low differentiation between the diploid populations for the gene flow 1.0285 according to the Wrights. Haploid and diploid populations are two populations located at different differentiation level. The data supplied support for selection of breeding strategy.The gametophytes, carposporophytes, and tetrasporophytes of Gracilaria lemaneiformis are difficult to distinguish prior to physiological appearance, because of their morphological similarity. The current method for distinguishing among is to wait for them to reach their natural maturity. In order to identify the sex of immature Gracilariopsis lemaneiformis, we used AFLP technique to search for possible sex- or phase-related markers in eight male gametophytes, female gametophytes, and tetrasporophytes with 7 primer combinations. The primer combination E-TG/M-CCA detected a specific band linked to female gametophytes and tetrasporophytes. The special DNA fragment was recovered and a 402bp fragment was sequenced. However, no perfect DNA sequence match was found in the public databases. SCAR primers were designed from the sequence to test the repeatability and stability of the relationship to sex, using new genomic DNA of 10 male gametophytes, female gametophytes, and tetrasporophytes.The test result demonstrated good linkage and repeatability. The SCAR primers developed in this work can reduce sex identification of Gracilariopsis lemaneiformis by a time of four to six months, which could improve the schedule for sexual breeding and other works related to the sex. |