Subfossil chironomids are regarded as a useful biological proxy for palaeoenvironmental research, but picking chironomid head capsules from aquatic sediments is extremely time-consuming. This is often the case for finding and isolating small head capsules from the deflocculated sediment. In this study, two stains (aniline blue and cotton blue) were used to dye chironomid head capsules in lake and peat sediments to improve the traditional pretreatment method and boost the picking efficiency. The results suggested that: (1) there were sharp contrasts between chironomids and residues after staining, which could shorten picking time for both lake and peat samples; (2) different parts of head capsules showed distinctive colour in stained samples and thus facilitated identification and taxonomy of subfossil chironomids; (3) the dyeing effects of two stains were comparable and no significant effect of staining on chironomid composition has been observed compared with unstained samples. This study demonstrates that aniline blue and cotton blue stain can promote picking efficiency of subfossil chironomids, and can be widely applied to pretreatment of sedimentary chironomids in palaeoenvironmental studies on lakes and peatlands.