The relationship of the genes of PAL (phenylalanine ammonia-lyase) and scopoletin was explored to reveal the key gene involved in PAL activity, PAL expression and scopoletin accumulation in noni (Morinda citrifolia L.) leaves and fruit. Our results display how the enzyme activity of PAL in noni fruit and leaves increases gradually with the leaves maturity, and exogenous ethephon induces PAL activity in noni leaves, which is consistent with the scopoletin accumulation law. Based on our previous transcriptome data, three PAL fragments were retrieved, and their full lengths were cloned via RACE; named as McPAL1, McPAL2 and McPAL3. The analysis of qRT-PCR showed that McPAL3 is expressed in the leaves and mature fruit, McPAL2 in the leaves only and McPAL1 mainly in the young stage of fruit. Ethephon induced the expression of McPAL2 and McPAL3 in the leaves, and McPAL1 and McPAL3 in the fruit. In noni fruit treated with ethephon, the expression pattern of McPAL3 was consistent with the trend of the scopoletin content and total PAL activity. We conclude that McPAL3 is the key gene involved in the accumulation of scopoletin, which can be induced by ethylene (ETH).