Infestations of head lice continue to be a serious public health issue, notably in Egypt. For the implementation of efficient management measures, accurate species identification and researching their treatment approaches became crucial. So, the purpose of this research was to examine the morphological structure of Pediculus humanus capitis (P. h. capitis) using scanning electron microscopy (SEM) as a foundational study for further investigation into the function of sensory structures and their significance in the host choice. As well as it aimed to study the evolutionary relationships between P. h. capitis populations through the analysis of cytochrome c oxidase subunit I (COI) gene sequences, subsequently investigating the host's pediculicide resistance. Participants from Menoufia Governorate, Egypt provided head lice sample specimens. SEM analysis provided detailed insights into the external morphology of P. h. capitis, elucidating its features. The resulting COI sequences of Egyptian lice were investigated comparing them with those in different countries. In addition, molecular assessment of topical preparations of pediculicides (malathion, permethrin, phenothrin, and ivermectin) and garlic oil was performed after one and three weeks of treatment of the lice-infested individuals. Acetylcholine esterase (AChE), glutathione-s-transferase (GST), and cytochrome P450 (CYP450) gene expression were used to evaluate the efficacy of anti-lice preparations. The results of this study revealed that SEM of P. h. capitis indicated morphological features that could help in further studying the functions of sensory structures. In addition, phylogenetic analysis revealed that the Egyptian samples clustered together with head lice populations from Asia and Africa.  Also, it was noticed that increased transcriptional levels of CYP450, AChE, and GST genes in malathion, permethrin, and phenothrin-treated groups suggested some level of resistance to these agents. While ivermectin and garlic oil were recommended at the same time as efficient substitutes. In conclusion, the COI gene sequences of P. h. capitis in Egypt are phylogenetically related to other countries. Additionally, molecular analysis revealed that several of the regularly used pediculicides result in resistance in the infested individuals.