Ikan cakalang (Katsuwonus pelamis Linnaeus, 1758) merupakan salah satu sumberdaya ikan pelagis besar yang mempunyai nilai ekonomis penting. Informasi mengenai struktur ukuran dan beberapa parameter populasinya masih sangat terbatas khususnya di perairan Indonesia timur. Penelitian ini dilakukan di Morotai, Biak dan Jayapura dari Januari sampai Desember 2013. Tujuan penelitian ini adalah untuk menganalisis ukuran ikan yang tertangkap dan menganalisis parameter populasi meliputi laju pertumbuhan, mortalitas dan tingkat eksploitasi. Estimasi parameter pertumbuhan, mortalitas dan laju eksploitasi dihitung menggunakan program FiSAT (FAO-ICLARM Stock Assessement Tools). Ukuran ikan cakalang hasil tangkapan pancing tonda dan pancing ulur berkisar antara 15 – 94 cmFL (Fork Length), dengan modus antara 40-45 cmFL. Ukuran pertama kali tertangkap sebesar 40,1 cmFL dan kebanyakan adalah ukuran ikan yang sedang memijah. Hasil analisis menggunakan FiSAT II diperoleh laju pertumbuhan (K) sebesar 0,41/tahun, panjang asimptotik (L) 101,85 cmFL. Laju kematian alami (M) 0,6 / tahun, laju kematian karena penangkapan (F) 0,62 /tahun dan laju mortalitas total (Z) 1,22 /tahun. Tingkat eksploitasi ikan cakalang hampir fully exploited (E= 0,46). Disarankan tidak perlu ada penambahan upaya penangkapan atau status quo untuk menjaga agar sumberdaya ikan cakalang tetap terjaga kelestariannya. Skipjack tuna (Katsuwonus pelamis Linnaeus, 1758) is one of the large pelagic fish resources which have high economic value. Information on the size structure and population parameters is still limited especially in the waters of eastern Indonesia. The Research was conducted from January to December 2013 at Morotai, Biak and Jayapura. The aim of this study was to analyze the size of the fish caught and some of population parameters such as the growth rate, mortality rates, and exploitation rate. Estimated of growth parameters, mortality and exploitation rate using the program FiSAT (FAO-ICLARM Stock Assessement Tools). The size of skipjack tuna caught by troll line and handline in between 15-94 cmFL, with a mode of 40-45 cmFL. The Length at first capture was 40.1 cmFL, most of them had condition of spawning. By using program FiSAT II analysis resulted that growth rate (K) of skipjack tuna was 0.41/year, with length asimptotik (L) reaches 101.85 cmFL. The natural mortality rate (M) was 0.6 / year. The fishing mortality rate (F) was 0.62 / year and total mortality rate (Z) was 1.22 / year. The exploitation rate of skipjack tuna was nearly fully exploited (E = 0.46). It was recommended the exploitation rate of this fish should be no additional effort (status quo) to keep sustainability of the skipjack tuna resource.