Tropical and subtropical Caulerpa species are epidemic to northern and southern Taiwan seashore. We here describe the molecular characteristics of rRNA gene, including the internal transcribed spacers (ITS) in this genus and a comparison was made with associated species sequences registered in the GenBank. A total of nine specimens (C. racemosa var. microphysa, macrophysa, peltata, laetevirens, C. serrulata and C. elongata.) was investigated. Samples were collected and distinguished first from morphological characteristics. The genomic DNA was individually extracted using CTAB protocol. To amplify the 18S rRNA, ITS1, 5.8S rRNA, ITS2 and 28S rRNA sequences, a primer pair NS7 and ITS4, sequences located in nuclear rRNA region, was used. The range of 980-1100bp DNA fragment from genomic DNA of individual plant was generated from polymerase chain reaction (PCR). Amplified fragments were sequenced automatically with ABI sequencer. The sequences were aligned with those of other Caulerpa species retrieved from the GenBank. The phylogenetic tree was constructed using Clustal method. The comparison of whole sequence and 18S rRNA and ITS1 region among these specimens shows that the inter-species divergence within C. racemosa var. microphysa, macrophysa, peltata and laetevirens is larger than those of intra-species of C. taxifolia, C. serrulata and C. elongata. It is supposed that they (C. racemosa var. microphysa, macrophysa, peltata and laetevirens) should be in the position of different species in Caulerpa genus from the present rRNA sequences analysis. The sequences of 5.8S region are shown more conserve than that of 18S region. The identity of ITS1 and ITS2 regions in present species are low, comparing with C. taxifolia, C. maxicana.

Key words: Caulerpa, internal transcribed spacer (ITS)., rRNA gene