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Simple Summary: As the most diverse vertebrate group, the unique adaptive expansion of euryhaline fishes is critical to understanding vertebrate evolution. In particular, the high degree of consistency of unique paired appendage structures across the extremely morphologically diverse group of teleost fishes has become a fascinating scientific question. Early teleost fishes provide a critical window into the study of this large taxon. Therefore, this study constructs high-quality chromosome-level genomes of Osteoglossiformes (Chitala ornata). It also explores the genomic features of early teleost fishes and traces the unique genetic basis of pectoral fin evolution in teleost fishes at the molecular level, which provides an important basis for understanding the evolution of the origin of early teleosts. Teleosts are the most prolific vertebrates, occupying the vast majority of aquatic environments, and their pectoral fins have undergone remarkable physiological transformations throughout their evolution. Studying early teleost fishes, such as those belonging to the Osteoglossiformes order, could offer crucial insights into the adaptive evolution of pectoral fins within this group. In this study, we have assembled a chromosomal-level genome for the Clown featherback (Chitala ornata), achieving the highest quality genome assembly for Osteoglossiformes to date, with a contig N50 of 32.78 Mb and a scaffold N50 of 40.73 Mb. By combining phylogenetic analysis, we determined that the Clown featherback diverged approximately 202 to 203 million years ago (Ma), aligning with continental separation events. Our analysis revealed the intriguing discovery that a unique deletion of regulatory elements is adjacent to the Gli3 gene, specifically in teleosts. This deletion might be tied to the specialized adaptation of their pectoral fins. Furthermore, our findings indicate that specific contractions and expansions of transposable elements (TEs) in teleosts, including the Clown featherback, could be connected to their adaptive evolution. In essence, this study not only provides a high-quality genomic resource for Osteoglossiformes but also sheds light on the evolutionary trajectory of early teleosts. [ABSTRACT FROM AUTHOR]