This study focuses on the REM, RAV, ARF, and LAV families of B3 DNA-binding superfamily genes in sponge gourds. Through in silico genome-wide analyses, the study identifies these families and highlights the absence of ABI3 and HSI families, indicating distinct evolutionary adaptations. Different forms of the REM, ARF, and LAV families suggest that their functions change during different stages of development or in response to environmental factors. The study identifies a total of 52 B3 genes and categorizes them into four classes: ARF, REM, LAV, and RAV. Physicochemical investigation reveals that the protein is hydrophilic and located in the nucleus. Phylogenetic analysis shows distinct clades specific to each class based on sequence similarity. Gene duplication patterns across chromosomes reveal evolutionary dynamics, while analysis of gene architecture and conserved motifs emphasizes diverse functional roles. Structural and phosphorylation analyses provide insights into protein function, and expression profiling reveals tissue-specific roles. Overall, this study provides a molecular framework for understanding the functional analysis of B3 genes in sponge gourds, particularly during fruit development. It also contributes valuable information about protein properties and tissue-specific functions, improving our understanding of the dynamics of the B3 gene family in sponge gourds.