Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 8 sexual and 8 asexual isolates of D. pulex from whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer common (fixed) TE insertions, and in the mean time, demonstrate higher insertion polymorphisms than in asexual clones, supporting the hypothesis that sexual reproduction facilitates the spread of TEs while limiting the deleterious load imposed by TE insertions. We identified a subset of asexual-specific TE insertions, including the insertions of 20 LTR retrotransposons, two non-LTR retrotransposons and five DNA transposons. By comparison, no sexual-specific TE insertions were observed in our analysis. Furthermore, 24 out of the 27 asexual-specific insertion sites are located in contigs from chromosomes VIII, IX, and X that are known to be associated with obligate asexuality in D. pulex and partially derived from D. pulicaria. We found that 18 out of the 27 asexual-specific TE insertions can also be detected in some D. pulicaria isolates, indicating only a small number of TE insertions have likely accumulated after the origin of obligate asexuals.