The reaction of the molybdenum alkylidyne complex [MesC≡Mo{OC(CF3)3}3] (MoF9, Mes = 2,4,6-trimethylphenyl) with the potassium siloxides KOSi(OtBu)3 and KOSi(OtBu)2(OMes) furnished the mixed fluoroalkoxy-siloxy alkylidyne complexes [MesC≡Mo{OC(CF3)3}2{OSi(OtBu)3}] (MoSiF9) and [MesC≡Mo{OC(CF3)3}2{OSi(OtBu)2(OMes)}] (MoSi*F9). Treatment of MoF9, MoSiF9 and MoSi*F9 with an excess of 3-hexyne (EtC≡CEt) afforded labile metallacyclobutadiene (MCBD) complexes with a (C3Et3)Mo core, which are in equilibrium with the corresponding propylidyne (EtC≡Mo) complexes in solution. Thermodynamic parameters for these [2+2]-cycloaddition/cycloreversion reactions were determined by van 't Hoff plots, revealing that the nature of the ancillary siloxide ligand exerts a significant effect on the MCBD stability. X-ray diffraction analysis of MoSi*F9-MCBD provided the first accurate crystal structure of a molybdenacyclobutadiene (MoCBD). MoF9, MoSiF9 and MoSi*F9 proved active catalysts for the metathesis of internal alkynes and diynes, with MoSi*F9 showing unprecendented selectivity in the conversion of sterically encumbered 1,3-pentadiynes into symmetrical 1,3,5-triynes and 2butyne.