For successful sterile insect technique (SIT), synchronized copulation between invaded females and sterilized males is required. Understanding the mating time of the invaded strain is an aid in synchronizing and thus improving the effectiveness of SIT. We previously demonstrated a relationship between variation at two sites of a circadian clock gene cryptochrome (cry) (cry1212 and cry1865) and circadian behavior in the melon fly Bactrocera cucurbitae (Coquillett). Here we investigated the relationship in two other populations, Taiwan1 (T1) and Taiwan2 (T2), which may re-invade Okinawa. The results showed that T1 exhibited a lower frequency of the S-type allele, which was observed in early mating flies in the strains in Okinawa, than T2 at the site of cry1212. In addition, T1 showed a longer circadian period than T2. We also noted that the cry1212 site showed higher amino acid sequence conservation than cry1865 by comparing CRY1 among five insect species. These results suggest that genotyping of only the cry1212 site of trapped flies enables an immediate estimate of the mating time of the B. cucurbitae population from Taiwan and that cry1212 would be more likely to be involved in determining the mating time than cry1865.