My example: Sequence of HBB (Hemoglobin Beta) in Fishes.
How can I do a good search to obtain above sequences in NCBI? (I know hot to download them into a FASTA file)
Try going to http://www.ncbi.nlm.nih.gov/protein and searching for ' (hemoglobin beta[Protein Name] OR (hemoglobin[All Fields] AND beta[All Fields])) AND "Fish"[ORGN] '.
Search filters can be changed with the panel to the left of the search results.