Comparison of closely related genotypes from populations with distinct population sizes can help us understand the impact of effective population size on genome evolution. For this purpose, we present a high-quality genome assembly of Daphnia pulex (PA42) and perform comparative analysis with the previously sequenced genome of Daphnia pulex (TCO) in the same species. PA42 is similar with TCO at the orthologous gene level, with average protein identity 98.8% and more than 60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the genome annotation of TCO, with ~8,000 excess of the genes being due to inclusion of genes of bacterial origin or inaccurate annotation . This view is supported by the high GC content, lack of introns, and high sequence coverage of these suspicious genes. The reduced effective population size of the source population of TCO relative to that of PA42 makes the comparison of these two genomes an excellent platform to understand the short-term impact of effective population size on eukaryotic genome architecture. Consistent with the view that reduced effective population size can facilitate the fixation of transposable elements (TEs) and newly gained introns, we observe more proliferation of TEs and higher frequency of gained introns in the TCO genome.