An extremely unorthodox method of chromosome segregation is found in sciarid flies (Diptera, Sciaridae), where at male meiosis, the whole paternal complement is eliminated and the maternal X chromosome undergoes non-disjunction. At meiosis I, a monopolar spindle directs the segregation of maternal chromosomes to the single pole, whereas paternal chromosomes are discarded. At meiosis II, although maternal autosomes segregate normally, the X chromosome remains undivided. A cis-acting locus within the heterochromatin proximal to the centromere is known to regulate X centromere activity. By immunofluorescence analysis in spermatocytes from Sciara ocellaris and Sciara coprophila, we investigated histone H3 phosphorylation at Ser10, Ser28, Thr3 and Thr11 during male meiosis. We found that chromosome condensation and H3 phosphorylation patterns differ between chromosomes of different parental origin at the time of paternal set elimination. Importantly, at meiosis II, the maternal X chromosome differs from the rest of the chromosomes in that its centromeric region does not become phosphorylated at the four histone H3 sites. We provide here the first evidence linking the under-phosphorylated H3 status of the X chromosome centromeric region with its meiotic non-disjunction in sciarid flies. Our findings strongly support the idea that the deficiency in local H3 phosphorylation inactivates the X centromere at the transition from meiosis I to meiosis II.