Malaria continues to be a global health problem, with the female Anopheles gambiae mosquito serving as the major vector. To better combat this devastating disease, understanding mosquito physiology is essential. Numerous studies demonstrate the importance of small non-coding RNAs (ncRNAs) in several aspects of mosquito physiology. To obtain a global detailed insight of ncRNAs in Anopheles gambiae, we systematically classified multiple small ncRNA groups across mosquito tissues. Using small RNA-Seq analysis, we determined ncRNA transcriptomes in tissues critical for mosquito reproduction and immunity including fat body-abdominal wall enriched tissues, midguts, ovaries, and remaining tissues comprised of the head and thorax. Our work (i) determined microRNA (miRNA) expression patterns between tissues, (ii) updated the piRNA annotation in ovaries, (iii) identified pan-tissue and tissue-enriched mRNA-derived small ncRNAs, and (iv) assessed AGO1- and AGO2- loading of candidate small ncRNAs using publically available datasets. Additionally, our recent work identified a cluster of miRNAs upregulated after blood-feeding, illustrating the dynamic responses of small ncRNAs across physiological processes. Our goal is to build a foundation for future research concerning the relationships between small ncRNAs, mosquito physiology, and vector-borne disease transmission.