To obtain a clearer understanding of the evolutionary transition between short- and long-germ modes of embryogenesis in insects, we studied the expression of two gap genes hunchback (hb) and Krüppel (Kr) as well as the pair-rule gene even-skipped (eve) in the dipteran Clogmia albipunctata (Nematocera, Psychodidae). This species has features of both short- and long-germ mode of embryogenesis. In Clogmia hb expression deviates from that known in Drosophila in two main respects: (1) it shows an extended dorsal domain that is linked to the large serosa anlage, and (2) it shows a terminal expression in the proctodeal region. These expression patterns are reminiscent of the hb expression pattern in the beetle Tribolium, which has a short germ mode of embryogenesis. Krüppel expression, on the other hand, was found to be rather similar to the Drosophila expression, both at early and late stages. eve expression starts with six stripes formed at blastoderm stage, while the seventh is only formed after the onset of gastrulation and germband extension. Surprisingly, no segmental secondary Eve stripes could be observed in Clogmia although such segmental stripes are known from higher dipterans, beetles and hymenopterans. We therefore also studied another nematoceran, Coboldia, to address this question and found that some segmental stripes form by intercalation as in Drosophila, although belatedly. Our results suggest that Clogmia embryogenesis, both with respect to morphological and molecular characteristics represents an intermediate between the long-germ mode known from higher dipterans such as Drosophila, and the short-germ mode found in more ancestral insects.