This study was carried out to obtain useful information on the cost-effective and labor-saving methods in the on-farm pigmented rice cultivation trials that were performed in Gangjn, Jindo and Gimje provinces. Two different pigmented rice cultivars were tested at each site from 2014 to 2015. From the common rice transplant technologies, Wet Hill Direct Seeding Technology (WHDST) was applied and was compared to Transplanting Machine (TM) Technology, which was mainly used for rice transplanting. The results of the study showed that during the trial period, the average C3G contents of pigmented rice ‘Heugkwang’ in Gangjin was 145.5 mg/100g using the WHDST. This was 23.5 mg/100g higher than using TM in Gangjin area. On the other hand, the C3G contents of functional pigmented rice variety ‘Seonhyangheukmi’ was 163 mg/100g under the WHDST while 189.3 mg/100g under the TM. Therefore, it was observed that the C3G contents of functional pigmented rice changed depending on the variety and according to the annual environmental variation. In Jindo area, two years average C3G contents of functional pigmented rice variety ‘Josaengheugchal’ was resulted to 268.1 mg/100g using TM. This C3G contents was 97.8 mg/100g more than the amount obtained using WHDST. For functional pigmented rice variety ‘Shinnongheugchal’, the C3G contents was 247.3 mg/100g in the WHDS, while 249.1 mg/100g in the TM. This indicated that C3G contents tended to be similar based on cultivation method. The C3G contents of the rice variety ‘Heugkwang’ in Gimje area were 34.7 mg/100 g and 20.2 mg/100g using WHDST and TM, respectively. Meanwhile, the C3G contents of functional pigmented rice variety ‘Heugsujeong’ was 85.6 mg/100g in the WHDST and 43.62 mg/100g in the TM. In conclusion, the study showed that the C3G contents of the pigmented rice are affected by the yearly environmental variation, the regions, and the cultivated variety.