Following the report of evaluation of growth performance of a new hybrid NEW GIFT Nile tilapia ♀ × blue tilapia ♂, this report dealing with a comparison analysis of morphological variations among this hybrid,its close hybrid (Nile tilapia ♀ × blue tilapia ♂), and their three parents(NEW GIFT Nile tilapia, Nile tilapia,and blue tilapia). ANOVA,cluster analysis,discrimination analysis and principle analysis were adopted,and 4 countable morphological parameters,9 meristic parameters,8 ratio parameters and 24 truss network parameters were used for a systematic analysis.The results are: (1) For countable parameters,there are no significant differences among NEW GIFT Nile tilapia ♀ × blue tilapia ♂ and other 4 genotypes tilapia.(2) For meristic parameters and truss network parameters,there are significant differences in 21 parameters of meristic plus network.(3) Cluster analysis and discrimination analysis indicated identically that,the hybrid(NEW GIFT Nile tilapia ♀ × blue tilapia ♂) is much close to their material NEW GIFT,and the hybrid(Nile tilapia ♀ × blue tilapia ♂) is much close to their maternal side,all show a strong maternal genetic influences on morphology of hybrids.(4) For the two very close hybrids(NEW GIFT Nile tilapia ♀ × blue tilapia ♂ and Nile tilapia ♀ × blue tilapia ♂) which are different at brooder strains level only.This study can identify the significant difference in morphology,and it indicates that the approach of this study,e.g.,combination of three kind of parameters (countable,meristical and truss network), three kind of statistical analysis (cluster, discrimination and principle analysis), can provide a strong and sensitive approach to morphological study on strain specific level.