Arthropods are one of the most abundant groups of animals with diverse lifestyle and habitats. Because of the different niches arthropods live in, arthropods are great organisms for studying gene family evolution. Given the great number of arthropod species, only a few arthropod species are model organisms with complete reference genomes. Taking advantage of the development of next generation sequencing techniques and bioinformatics, more and more arthropod genes, transcriptomes and genomes are available. This growing genomic data provides a great opportunity to study arthropod gene family evolution.   In this doctoral dissertation, I investigated the gene family evolution in three different systems. Firstly, I applied transcriptome sequencing on caddisfly species to understand the tetrodotoxin resistance and pyrethroid resistance of sodium channel genes. I found potential molecular mechanisms relating to tetrodotoxin and pyrethroid resistance. Secondly, I used transcriptome sequencing dataset of 1000 insect transcriptome project to understand the co-evolution between mitochondrial-encoded and nuclear-encoded oxidative phosphorylation (OXPHOS) genes. I found elevated nuclear OXPHOS gene evolutionary rate in Hymenoptera. Lastly, I investigated the mitochondrial-nuclear interaction in five different haplodiploid species across 500-million year of evolution. And I found elevated mitochondrial gene evolutionary rate in all the haplodiploid species. I also found fast-evolving random nuclear genes in Hymenoptera, indicating mixed pattern of mitochondrial-nuclear evolution in arthropods.  What follows are an introductory chapter, three data chapters, and a conclusion chapter where I summarized the findings in three systems and the future applications of comparative genomics on arthropod gene family evolution studies.