Parachromis managuensis is a native cichlid fish from Central America and is the most commonly traded species within its genus. This study presents the first chromosome-scale genome assembly of P. managuensis using PacBio HiFi long reads and Hi-C sequencing data. The size of the P. managuensis genome is approximately 896.66 Mb, with a scaffold N50 of 38.19 Mb. The assembled genome demonstrates high quality in terms of completeness and accuracy, with a BUSCO score of 98.85% and a quality value (QV) of 50.95. A total of 888.60 Mb (99.10%) sequences were anchored to 24 pseudochromosomes. Additionally, 21,145 protein-coding genes and 325.58 Mb (~36.31%) repetitive sequences were identified. This chromosome-level genome assembly provides a crucial reference for studying the evolution and ecological adaptability of P. managuensis.
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