Phosphonium and uronium salt-based reagents enable efficient and effective coupling reactions, and are indispensable in peptide chemistry, especially in machine-assisted solid phase peptide synthesis (SPPS). However, after the activating and coupling steps with these reagents in the presence of tertiary amines, Fmoc derivatives of Cys are known to be considerably racemized during their incorporation. To avoid this side reaction, a coupling method mediated by phosphonium/uronium reagents with a weaker base, such as 2,4,6-trimethylpyridine (TMP), than the ordinarily used N,N-diisopropylethylamine (DIEA) or that by carbodiimide has been recommended. However, these methods are appreciably inferior to the standard protocol applied for SPPS, i.e. a 1-min preactivation procedure of coupling with phosphonium or uronium reagents/DIEA in DMF, in terms of coupling efficiency and also, the former method cannot reduce racemization of Cys(Trt) to an acceptable level (< 1.0%) even when the preactivation procedure is omitted. Here, the 4,4’-dimethoxydiphenylmethyl (Ddm) and 4-methoxybenzyloxymethyl (MBom) groups were demonstrated to be acid-labile S-protecting groups that can suppress racemization of Cys to an acceptable level (< 1.0%) when the respective Fmoc derivatives are incorporated via the standard SPPS protocol of phosphonium or uronium reagents with the aid of DIEA in DMF. Furthermore, these protecting groups significantly reduced the rate of racemization compared to the Trt group even in the case of microwave (MW)-assisted SPPS performed at a high temperature.