Abstract: As an important horticultural crop worldwide, melon cultivation has been significantly affected by increasingly serious cultivations problems in recent years due to changes in cultivation systems and environment. Critical for continuous melon cultivation was allelopathy. However, little has been done in terms of the molecular biology of melon allelopathy. In this research, allelopathic autotoxicity genes of melon germplasm 'New Silverlit' were analyzed using the cDNA-AFLP technique. Seedlings were treated with 0.03 g·mL 1 concentrations of aqueous extracts from melon roots and stems for cDNA-AFLP analysis. A total of 3 600 transcript-derived fragments (TDFs) were obtained via cDNA-AFLP with 82 primer pairs. Each primer pair was amplified to 30~50 bands with fragment size of 50~800 bp. The TDF expression patterns were divided into four ― up-regulation, down-regulation, transient-expression and continuous-expression. From 103 selected TDFs, 75 had reliable sequences. Also 55 (73%) of the reliable TDF sequences functions were determined through BLAST search in GenBank database. Most of the 55 TDF genes involved in energy and metabolism (17.31%), signal transduction and regulation (15.38%), protein synthesis and ion transport (34.62%) and disease defense (32.69%) were predictable. Of the 75 reliable TDFs, 10 homologous genes were critical for disease defense conditions and signal transductions. Uncharacterized genes were validated in cDNA-AFLP expression patterns using semi-quantitative reverse-transcription polymerase chain reaction (PCR) analyses. This analysis used melon actin as the internal reference gene. The cDNA-AFLP technique confirmed altered expression patterns of 9 (90%) genes. The results show that cDNA-AFLP was a reliable technique for analyzing expression patterns of genes involved in melon allelopathy. Genes involved in melon allelopathy were identified and their expression patterns determined. This study was helpful in shedding more light on molecular mechanisms of melon allelopathy. It was also useful in identifying genes that could alleviate allelopathic autotoxicity in melon.