Most extant cyanobacteria contain C16 fatty acids in the sn-2 positions of glycerolipids, which are regulated by lysophosphatidic acid acyltransferase (LPAAT; EC 2.3.1.51). Synechocystis sp. PCC6803 contains sll1848, sll1752, and slr2060 as putative acyltransferase genes. sll1848 was recently reported to encode an indispensable palmitoyl-specific LPAAT; however, here we show that each of the three genes is dispensable. D1848 and D1848 D2060 cells had markedly higher contents of stearate (18:0), oleate (18:1), and linoleate (18:2) in place of palmitate (16:0) in the sn-2 positions, suggesting that D1848 D2060 cells incorporate 18:0 and 18:1 in the sn-2 positions. The levels of sll1752 transcripts increased in D1848 D2060 cells. This was accompanied by increased LPAAT activity toward 18:0 coenzyme A and its derivative in the membrane fraction. From these findings, together with the activity of a recombinant sll1752 protein and complementation of the Escherichia coli LPAAT mutant plsC, we conclude that sll1752 encodes a second LPAAT that prefers stearoyl and oleoyl substrates. D1848 D2060 cells grew slowly at 30°C at lower cell density, and exhibited more severe damage at 20°C than wild-type cells. Furthermore, D1848 D2060 cells exhibited photoinhibition more severely than wild-type cells. A phycobilisome core-membrane linker protein (slr0335) was also found to be susceptible to protein extraction under our conditions; its content decreased in the membrane fractions of D1848 D2060 cells. We conclude that C16 fatty acids in sn-2 positions are preferred in the photosynthetic growth of this cyanobacterium, despite sll1752 orthologs being conserved in most cyanobacteria. However, no sll1752 ortholog is conserved among photosynthetic eukaryotes including Cyanidioschyzon merolae.