Past evidence has indicated that Mycobacterium gordonae, as isolated from soil and as an occasional opportunistic pathogen, exists as a serocomplex. We now demonstrate that the basis of seroreactivity and diversity is a novel series of alkali-labile, trehalose-containing lipooligosaccharides (LOS). The structures from two strains were established by per-O-methylation, partial acid hydrolysis, infrared and high-field NMR spectroscopy, electron-impact MS, and fast atom bombardment/mass spectrometry of the native lipooligosaccharides and hydrolysis products. The structure of the major lipooligosaccharide, LOS-I, of M. gordonae strain 989 was defined as 2-O-CH3-4-O-CH3CO-alpha-L-Fucp-(1-->3)-beta-D-Glcp-(1-->3)-2-OCH3-alpha-L-Rhap (1-->3)-[beta-D-Xylp-(1-->2)-]-alpha-L-Rhap-(1-->3)-beta-D-Glcp-(1-->3)-alpha-L-Rhap-(1-->3)-6-O-CH3-alpha-D-Glcp-(1<->1)-2,3,4,6-tetra-O-acyl-alpha-D-Glcp, which was further glycosylated at C-3 of the terminal 2-O-CH3-4-O-CH3CO-alpha-L-Fucp by an incompletely defined N-acyl derivative of 4-amino-4,6-dideoxy-2,3-di-O-CH3-Galp. The structure of the major lipooligosaccharide, LOS-I, of a second strain of M. gordonae (strain 990) was defined as alpha-L-Rhap-(1-->2)-3-O-CH3-alpha-L-Rhap-(1-3)-[beta-D-Xylp-(1-2)-]-alpha-L-Rhap (1-->3)-beta-D-Glcp-(1-->3)-beta-D-Glcp-(1-->3)-alpha-L-Rhap-(1-->3)-6-O-CH3-alpha-D-Glcp-(1<->1)-2,3,4,6-tetra-O-acyl-alpha-D-Glcp. The other minor LOSs from both strains were also defined. Both families of LOSs from the two strains contain a novel mono-6'-O-CH3-2,3,4,6-tetra-O-acyltrehalose unit, representing the first example of such a unit among the LOSs isolated to date from mycobacteria. Also, the more polar antigenic products, LOS-I, -II', -II'', and -III from M. gordonae 989 and LOS-I, -II, and -II' from M. gordonae 990, are characterized by branching of the oligosaccharide backbone, the first instance of sugar branching in these products. In the case of LOS-I and -III from M. gordonae 989, the branch consists of a terminal (t)-beta-D-Xylp unit, whereas in LOS-II' and -II'', they are (t)-3-O-CH3-beta-D-Xylp and (t)-alpha-D-Araf, respectively. Similarly, the more polar antigenic glycolipids of M. gordonae 990 are characterized by branching in the oligosaccharide backbone, a single terminal beta-D-Xylp residue in the case of LOS-I and LOS-II', and an alpha-D-Araf unit in LOS-II''. In some members of the LOS family, the unique branching of the oligosaccharide backbone was absent. The LOSs reacted strongly with antiserum raised against the homologous strain and only weakly against that to the heterologous strain, demonstrating that M. gordonae, like the Mycobacterium avium complex, is a serocomplex, but based on the trehalose-containing LOSs rather than the glycopeptidolipids.