The ethylene antagonist 1-methylcyclopropene (1-MCP) was investigated for its potential impact on the transcription of key flavonoid biosynthetic (PAL and CHS) and ethylene perception (ERS1) genes during the postharvest storage of pear (Pyrus × communis L.). Optimally harvested red and green `d'Anjou' fruit were treated with 1 μL·L-1 1-MCP for 24 h at 0 °C to 1 °C, and subsequently placed in cold storage (0–1 °C, 90–95% RH). Fruit were removed every 21 days for 126 days, and evaluated for firmness, TSS, and ethylene and volatile production for up to 10 days (≈21 °C). Tissue samples were collected for Northern blot analysis and determination of flavonoid and chlorogenic acid content. PAL content increased during the 1-week simulated marketing period irrespective of storage duration, which coincided with an increase in respiration and ethylene content. Although it was still detectable, total PAL content was dramatically reduced by the 1-MCP treatment. CHS was abundant immediately after harvest and after removal from storage, but declined rapidly thereafter, and was not detectable after 1 week at room temperature. The 1-MCP treatment further exacerbated this decreasing trend in CHS content. ERS1 content appears to be stable throughout storage and the simulated marketing period, with levels lower in 1-MCP-treated fruit. These results suggest that 1-MCP significantly inhibits the transcription of key flavonoid and ethylene regulatory enzymes, possibly compromising the nutraceutical content of pear fruit. The increase in PAL with the concomitant decrease of CHS after removal from storage suggests a diversion of carbon from flavonoid compounds into simple phenols, such as chlorogenic acid.