MLSA is an initialism that can refer to a number of things:
Medical Laboratory Scientists' Association, an Irish trade union Ministry of Labour Staff Association, a former British trade union MLSA1 and MLSA2, genes required for mycolactone biosynthesis Multilocus sequence analysis, a molecular biology technique involving Multilocus sequence typing Museum and Library Services Act, that established the Institute of Museum and Library Services Mutual Logistics Support Agreement, an agreement signed in 2002 as part of Philippines–United States relations