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Conserving tuna stock, biological information of tuna larvae is essential for understanding spawning ground and spawning time. However, morphological identification of larval is difficult and often times questionable. Meanwhile, genetic identification is useful and helpful to confirm the morphological identification result. This study purpose is to confirm a morphological identification result with genetic identification and determine the tuna species exactly. Specimens used in this research were obtained from a survey conducted in the Banda Sea in October 2018. Samples were collected by a bongo net towed obliquely. Morphological identification is to the tribe level, regarding the key features of the meristic and morphometric. Small tissue fragment from each sample was also analysed for genetic purposes using amplification of mitochondrial control region. Phylogenetic analysis was then performed using Neighbour-Joining with 1000 bootstrap replication. Genetic distance between individual sequences calculated using Kimura 2-parameter methods. Sequences of Euthynnus affinis (AP012946), Katsuwonis pelamis (KM094133, KM261666, KM094145, KM605252, KM094135), and Petenia splendida (KJ914664) were generated from GenBank database, and added to the phylogenetic analysis for species comparison. Result of morphological identification is showed that the larvae having 37 to 42 myomeres, preopercular spine developed, moderate in depth, moderate to large head and eyes identified as a tuna larva (Thunnini). However, this morphological data is not supported by genetic result, which indicated that the samples were identified as K. pelamis, E. affinis, and P. splendida. The intraspecific pairwise genetic distance for each species of K. pelamis, E. affinis, and P. splendida is 4.4 %; 0.5 %; and 22.3%, respectively. Meanwhile, the average pairwise genetic distance between the three species ranges from 16.2% to 33.3%.