Jaw malformations imply an important problem during the commercial production of Seriola lalandi larvae and juvenile fish in Chile and New Zealand. Since the rate of malformations in other fish species has been associated with the content of long-chain PUFA (LC-PUFA) in neutral lipids of the diet, the relationship between body LC-PUFA and the rate of malformations, together with a transcriptomic analysis of genes related to the metabolism and transport of lipids in commercially produced S. lalandi larvae have been investigated in the present work. A total of 10 batches of S. lalandi larvae were obtained and cultured at about 22 °C following the protocols of a Chilean commercial hatchery during the spawning season. There were three larval batches that were collected in August (austral winter), three batches that were obtained in October (spring), and finally four spawning events that were obtained in December-January (spring-summer). The rate and type of jaw malformations, the profile of long-chain PUFA (LC-PUFA) of total lipids during larval culture, and the distribution of LC-PUFA were analyzed. Additionally, a transcriptome analysis related to lipid metabolism in 40-day-old larvae was performed. As a result, a decrease in the rate of malformations was recorded from August to December. DHA showed a steep decrease between days 1 and 10 of culture, probably due to the consumption of yolk sac lipids, but a higher proportional change was noted in larvae that hatched during August. The DHA content in polar lipids (PL) and neutral lipids (NL) of 40-day-old larvae increased from August to December, so that the abundance of DHA was higher in PL in larvae that hatched in December, but it was higher in NL in those larvae that hatched in October. In conclusion, the rate of jaw malformations was associated with the rapid decline in DHA during early larval life and the highest abundance of DHA in neutral lipids at the end of the larval life.