The complexity of some sexual reproductive systems in arthropods still leaves both their genetic and epigenetic determinism and their evolutionary significance poorly understood. Pseudoarrhenotoky is characterized by obligate fertilization and differential inactivation and/or elimination of paternal chromosomes in embryos that develop into males. Here, we investigate how the paternal genome is transmitted in a pseudoarrhenotokous mite, Neoseiulus californicus, using codominant genetic markers detected by DALP (direct amplification of length polymorphism). Transmission patterns of parental alleles through one and two generations are reported at four or five loci corresponding to four linkage groups. Our data provide strong evidence for selective elimination of the paternal genome among male tissues. Sperm contained maternal genes exclusively, whereas some male somatic tissues retained most if not all paternal chromosomes. No recombination between parental genomes prior to paternal genome elimination from the embryonic germ line was observed. These data allow a reinterpretation of previous phenotypic and cytogenetic observations in these mites, from which we suggest some relevant mechanistic and evolutionary implications. In addition, this is the first published study using polymorphic codominant loci detected by the recently developed DALP method.