The 1998–99 Lobos again started strong with a 12–1 record, reaching #11; they stood at 16–2 after beating #7 Arizona but then lost four of five, struggling on the road. Thomas averaged 18 points and 10 rebounds, Long 17 points and 6.5 boards. The team won seven of their last nine, both losses coming to #8 Utah, in Salt Lake and in the WAC tournament final. The Lobos advanced to the NCAA Tournament for the fourth straight season, garnering a nine-seed against Missouri. Thomas had his best NCAA performance with 20 points, 10 rebounds, and four blocks, while Long added 17 points and 12 rebounds and made the game-winning basket in the closing seconds. The Lobos then fell to eventual national champion Connecticut, shooting just 26%, to finish 25–9. Thomas was named All-WAC for the third time and finished his career as the second leading scorer and top rebounder in Lobo history. He was selected as the 22nd pick in the first round of the 1999 NBA draft by Houston and played for 11 seasons in the NBA.