Abstract: High quality RNA isolation from tomato fruit is a basically molecular biology studies of relative gene controlling quality、development and metabolism of tomato fruit. However, previous attempts to extract high quality RNA from tomato fruit using published protocols have proven to be unsuccessful, even the use of protocols developed for the extraction of RNA from other fruit tissue. RNA isolation from tomato fruit is difficult due to tomato fruit containing large amounts of polysaccharides, polyphenol which often coprecipitate and contaminate, RNA during the extraction，thereby affecting both the quality and quantity of RNA when using conventional protocols. Now some commercial kits have not been developed directly for the isolation of high quality RNA from tomato fruit. Here four methods were used to isolate functional RNA from tomato fruit, and the best one was screened out. Using this protocol we obtained good RNA yield (401.6--840.2μg/g) from different stage tomato fruit with low levels of polysaccharides, polyphenolic compounds and protein contaminants as determined by A260/A230 and A260/A280 respectively. Furthermore，this RNA was not degraded，as was demonstrated by visualizing the ribosomal RNA of the samples on 1.2％ agarose gel electrophoresis. The RNA is suitable for cDNA-AFLP, which demonstrated that RNA isolation protocol modified in this paper can be used to related molecular researches．