There is hardly any molecular marker or genetical protocol to separate sex at early stage of invertebrate, you have to depend on morphological characterization. The sexual selection depend on SRY-TDF factor, that may developed gonodal activation in early. But with out sacrificing those specimen it would not possible. may other experts have give you the true clue.   

Dear Davide,

I don't know if sex determination in amphipods has a genetic or environmental basis, but the Doublesex (Dsx) genes have been shown to play an important role in controlling sexual dimorphism in genetic sex-determining organisms such as nematodes, insects, and vertebrates. Recently, Kato et al. (2011)  identified two Dsx genes from Daphnia magna, a freshwater branchiopod crustacean that parthenogenetically produces males in response to environmental signals and showed that DapmaDsx1 exhibits sexually dimorphic differences in the abundance of its transcripts. During embryogenesis, expression of DapmaDsx1 was increased only in males and its transcripts were primarily detected in male-specific structures. 

Please find attached the paper for more details.

Have you checked if there is any information on karyotype morphology differences (rather than DNA or RNA) for males and females in amphipods? Maybe that would be and appropriate tool if there is sex determination related to e.g. X0 or XY systems in their chromosomes. 

Thanks Francesc. 

Yes i have checked but for this analysis I need of fresh amphipod. I would establish the sex in fixed amphipod.