Now Johnson is gone and Hopkins has shown just how good he can be as the team's clear-cut top option.
He's leading the NFL with 726 yards receiving and is on pace to break many of Johnson's franchise receiving records.
Hopkins led the team in 2014 with a career-best 1,210 yards receiving, but in many ways he was still playing second-fiddle to Johnson, the longtime face of the franchise who was released in March after 12 seasons with the Texans.
So does the 23-year-old feel a shift this season with Johnson playing in Indianapolis?
''I don't really want to talk about him too much because he's not here, but yeah obviously,'' Hopkins said.
Hopkins has thrived this season despite Houston flip-flopping between Brian Hoyer and Ryan Mallett at quarterback. He had 10 catches for 148 yards in a win over the Jaguars on Sunday to become the first player in NFL history with nine or more catches and 145 or more yards receiving in three straight games.
It was Hopkins' fourth straight 100-yard receiving game to tie Johnson for the longest such streak in team history. Hopkins' 2,738 yards receiving are second in franchise history in a player's first three seasons behind Johnson's 2,806 yards and he has 10 games remaining.
If Hopkins continues at his current pace he would finish the season with 1,936 yards receiving, which would surpass the franchise mark of 1,598 yards Johnson had in 2012.
Hopkins' 726 yards receiving through six games are the second-most in the NFL since 1960 behind the 785 yards Wes Welker piled up in 2011. Third on that list is Hall of Famer Michael Irvin, who had 712 in 1993.
Hopkins, who was selected as the AFC Offensive Player of the Week on Wednesday, isn't too keen on talking about his individual accomplishments with the team off to a tough start.
''Our record is 2-4, so there's nothing really to be too amazed about,'' he said when asked about his performance.
But the 27th overall pick in the 2013 draft is certainly OK with others raving about his work.
''Why not? I guess I'm doing historical stuff right now,'' he said. ''I guess you guys should be amazed.''
Along with leading the league in yards receiving he's also near the top in several other statistical categories. His 52 receptions rank second, his five touchdowns receptions are tied for second, his 42 first downs are the most in the league and his 15 receptions on third down lead all players.
His success, according to players and coaches alike, is a product of his hard work and dedication.
''He's got a great work ethic, and there's really no substitute for that, and I think that has a lot to do with where he is right now,'' coach Bill O'Brien said.
Hopkins is only 6 feet 1, but his hands are very large, measuring 10 inches from thumb to pinkie. His extra-large mitts allow him to make catches many receivers simply wouldn't be able to snag.
He had two catches on Sunday against Jacksonville using just one hand. The first came when he reached out with his left hand and grabbed a back-shoulder pass for 16 yards.
The second one that had everyone buzzing came when he trapped the ball with one hand against the side of his helmet for a 29-yard gain in the fourth quarter.
''We were sitting in there watching it the other day reviewing it,'' Hoyer said. ''And Arian (Foster) just starts clapping and he's like, `You're going to pretend like that wasn't just like the most amazing catch you've seen?' I mean it really is when you think about it.''
Both of those catches came near the sideline, showing an area Hopkins has been targeting for improvement.
''I had some plays earlier in the season taken away from me just from not being aware of where I was on the sideline,'' he said. ''That's one of my focuses and one of the things I want to work on. It showed this past week.''
Hoyer, who has the starting job back after being benched in the season opener, targeted Hopkins 15 times on Sunday to give him 89 for the season, which is the most in the NFL through six games since 1991.
Offensive coordinator George Godsey was asked if they plan to keep throwing his way that much.
''We'll see how the defense defends him each week,'' Godsey said. ''I think that's kind of our mentality. If he's open, which he's open quite a bit, then we'll throw him the ball.''
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