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Simple Summary: Long terminal repeat retrotransposons (LTR-RTNs) are vital in genome evolution and diversity. The compact genomes of Tetraodontiformes provide an excellent model for studying LTR-RTN dynamics. An analysis of the genomes of ten tetraodontiform species revealed a total of 819 full-length LTR retrotransposon sequences classified into nine families spanning four distinct superfamilies. Among them, the Gypsy superfamily displayed the highest level of diversity. Takifugu stood out for having the highest abundance of LTR families and sequences. Evidence of recent LTR-RTN activity and multiple invasions was observed in specific tetraodontiform genomes. This investigation provides valuable insights into the evolution of LTR retrotransposons and their impact on the structure and evolution of compact tetraodontiform genomes. This study aimed to investigate the evolutionary profile (including diversity, activity, and abundance) of retrotransposons (RTNs) with long terminal repeats (LTRs) in ten species of Tetraodontiformes. These species, Arothron firmamentum, Lagocephalus sceleratus, Pao palembangensis, Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, Takifugu rubripes, Tetraodon nigroviridis, Mola mola, and Thamnaconus septentrionalis, are known for having the smallest genomes among vertebrates. Data mining revealed a high diversity and wide distribution of LTR retrotransposons (LTR-RTNs) in these compact vertebrate genomes, with varying abundances among species. A total of 819 full-length LTR-RTN sequences were identified across these genomes, categorized into nine families belonging to four different superfamilies: ERV (Orthoretrovirinae and Epsilon retrovirus), Copia, BEL-PAO, and Gypsy (Gmr, Mag, V-clade, CsRN1, and Barthez). The Gypsy superfamily exhibited the highest diversity. LTR family distribution varied among species, with Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, and Takifugu rubripes having the highest richness of LTR families and sequences. Additionally, evidence of recent invasions was observed in specific tetraodontiform genomes, suggesting potential transposition activity. This study provides insights into the evolution of LTR retrotransposons in Tetraodontiformes, enhancing our understanding of their impact on the structure and evolution of host genomes. [ABSTRACT FROM AUTHOR]