ABSTRACTThe MC1R gene, which is responsible for most cases of red hair, affects other hair and skin colours and contributes to differences in pain sensitivity and consists of a single exon with a very high level of allelic heterogeneity. In this research, we show that the Oxford Nanopore Technology (ONT) offers a good alternative to study the MC1R sequence variation. MinION was used to sequence the 1590 bp MC1R exon and minimal promoter in a cohort of 126 subjects, including 65 red‐haired individuals, using the FLO‐MIN106 (R9.4) chemistry. Assigned DNA variants were validated using Ion Torrent technology provided with Ion Xpress Plus Fragment Library Kit and the Personal Genome MachineTM (PGMTM). We show that the use of the latest sequencing kit V14 together with the FLO‐MIN114 (R10.4.1) flow cell has eliminated the systematic errors observed with the previous chemistry and allowed reliable detection of short indels important for phenotypic inference. Importantly, the use of the algorithm implemented in the EPI2ME software enabled convenient and accurate read‐based phase determination which can be useful in data interpretation.