The ripening fruit of two loquat (Eriobotrya japonica Lindl.) cultivars with different levels of lignin accumulation provide an intriguing example of lignification in flesh tissue. Increase in firmness as a result of lignification in ripening red-fleshed Luoyangqing (LYQ) fruit was confirmed, whereas white-fleshed Baisha (BS) fruit softened without lignification. Six cDNAs associated with the lignification pathway, i.e. EjPAL1, EjPAL2 (phenylalanine ammonia lyase, PAL, EC 4.3.1.5), Ej4CL (4-coumarate: coenzyme A ligase, 4CL, EC 6.2.1.12), EjCAD1, EjCAD2 (cinnamyl alcohol dehydrogenase, CAD, EC 1.1.1.195) and EjPOD (peroxidase, POD), were cloned from flesh tissue of LYQ fruit. Expression profiles of the six corresponding genes differed greatly in different tissues, and during fruit development and ripening in both LYQ and BS cultivars. Associated activities of PAL, 4CL, CAD, and POD enzymes were also measured. CAD and POD enzyme activities and the expression of EjCAD1 and EjPOD genes were most closely associated temporally with lignification of loquat flesh tissue. Levels of EjCAD1 transcripts were particularly aligned with changes in lignification during ripening as modified either by ethylene treatment or low temperature conditioning. The two PAL genes showed different expression patterns during fruit development, with EjPAL1 strongly expressed in mature fruit and EjPAL2 only expressed in early stages of development. In addition, EjCAD1 expression was stimulated by low temperature and may contribute to low temperature injury in the fruit. Our integrated data on lignin, monolignol precursors, and associated enzymes and genes, provide a consistent model of fruit lignification.