Passiflora is a plant genus known for its extremely distinctive and colorful flowers and a wide range of genome sizes (over ten-fold variation). However, the relationship between differences in genome size and organization and the variations in flower size and morphology among Passiflora species remains largely unexplored. Here, we assembled a chromosome-scale genome of Passiflora foetida, which is a close relative of the commercial passionfruit P. edulis. While the genome of P. foetida contains a substantial proportion of repetitive elements (66.7% of 424.16 Mb), it possesses significantly fewer copies of long terminal repeat retrotransposons (LTR-RTs) compared to P. edulis (83.94% of 1278.14 Mb; 87.29% of 1241.66 Mb). The disparity in LTR-RTs is one of the main contributors to the differences in genome sizes between these two species and possibly in floral traits. Additionally, we observed variation in insertion times and copy numbers of LTR-RTs across different TE lineages. Then, by integrating transcriptomic data from 33 samples (eight floral organs and flower buds at three developmental stages) with phylogenomic and metabolomic data, we conducted an in-depth analysis of the expression, phylogeny, and copy number of MIKC-type MADS-box genes and identified essential biosynthetic genes responsible for flower color and scent. Our study provides new insights on genome size variation and the evolution of flower development in two important Passiflora species.