Fresh fruit of longan (Dimocarpus longan Lour.) are susceptible to pericarp browning and aril breakdown. Aril breakdown in longan fruit is regarded as one of the most important factors reducing quality and shortening storage life of the fruit. To better understand the molecular mechanism of aril breakdown, the expression patterns of three expansin (EXP) and three xyloglucan endotransglucosylase (XET) genes in relation to the aril breakdown of longan fruit stored at room temperature (25 °C) or low temperature (4 °C) were investigated. The results showed that aril breakdown index increased progressively during storage at 25 and at 4 °C. Northern blotting analysis revealed that the accumulations of three EXP and three XET genes exhibited differential characteristics with the occurrence of aril breakdown. During storage at 25 °C, the accumulations of Dl-XET3 increased after 1 day, suggesting that Dl-XET3 correlated well with the early aril breakdown, while Dl-EXP3 together with Dl-XET1 and Dl-XET2 was involved in later aril breakdown. However, expression of Dl-XET1 and Dl-XET2 could be mainly involved in aril breakdown of longan fruit stored at 4 °C. In addition, Dl-EXP2, whose accumulation increased sharply when longan fruit were transferred from low temperature to room temperature within 12 hours, was related to the aril breakdown in this storage period. These data indicated that Dl-EXPs and Dl-XETs were closely related to aril breakdown in longan fruit.