To date, it is not known whether animal breeding values in Asian seabass (Lates calcarifer) can be estimated using single nucleotide polymorphisms (SNPs) generated from new high-throughput genotyping by sequencing platforms. The principal aim of the present study was to assess the genomic prediction accuracy for growth traits, survival, cannibalism, and disease resistance against Streptococcus iniae in this species L. calcarifer. Additionally, this study attempted to identify markers associated with the five traits studied as well as to understand if the genotype data can be used to estimate genetic parameters for these complex traits. The genomic best linear unbiased prediction (gBLUP) method was used to analyze 11,084 SNPs and showed that the prediction accuracies for growth traits (weight and length) were high (0.67–0.75). By contrast, these estimates for survival were low (0.25). Multi-locus mixed model analyses identified four SNPs significantly associated with body weight (p < 5 × 10−8 or −log10 p ≥ 5). There were, however, no significant associations detected for other traits. Similarly, the SNP heritability was moderate, while the estimates for other traits were approximated to zero and not significant. Genetic correlations between body weight and standard length were close to unity. Collectively, the results obtained from this study suggest that genotyping by sequencing platforms can provide informative DNA markers to conduct genome-wide association analysis, estimation of genetic parameters, and evaluation of genomic prediction accuracy for complex traits in Asian seabass.