An investigation of local citrus genetic resources grown on the Chuuk Islands of the Federated States ofMicronesia was conducted in August 2013. A total of 21 accessions were examined. According to the morphological traits, ten, four, four, two, and one accession resembled lime (local name "Nayimis"), sour orange ("Kurukur"), calamondin ("Tangerin" and "Gunkan"), sweet orange ("Kurukur" and "American Kurukur"), and pummelo ("Kurukur"), respectively. Next, cleaved amplified polymorphic sequence (CAPS) analysis was conducted. Then, precise accession identification was made based on the results of CAPS analysis in conjunction with morphological traits. "Nayimis" accessions were classified into at least two types. Genotypes of "Nayimis" type 1 were identical to those of Mexican lime. A genetic influence from mandarin was detected in "Nayimis" type 2. Although the morphological traits of all "Kurukur" sour orange types were similar, their diversity was revealed by CAPS analysis. The genotype of one "Kurukur" accession was identical to that of sour orange. Genotypes of the sweet orange-type "Kurukur" and "American Kurukur" were different. The types of "American Kurukur" and sweet orange were the same. Pummelo-type "Kurukur" was considered to be true pummelo based on the results of morphological and molecular markers. Morphologically, the calamondin-like accessions "Tangerin" and "Gunkan" showed the same genotype combinations on CAPS analysis. These genotypes were identical to those of calamondin used as a control. The combined results of morphological and molecular markers offer valuable information for the identification of citrus genetic resources on the Chuuk Islands.